Network dynamics and systems biology

NASA Astrophysics Data System (ADS)

Norrell, Johannes A.

The physics of complex systems has grown considerably as a field in recent decades, largely due to improved computational technology and increased availability of systems level data. One area in which physics is of growing relevance is molecular biology. A new field, systems biology, investigates features of biological systems as a whole, a strategy of particular importance for understanding emergent properties that result from a complex network of interactions. Due to the complicated nature of the systems under study, the physics of complex systems has a significant role to play in elucidating the collective behavior. In this dissertation, we explore three problems in the physics of complex systems, motivated in part by systems biology. The first of these concerns the applicability of Boolean models as an approximation of continuous systems. Studies of gene regulatory networks have employed both continuous and Boolean models to analyze the system dynamics, and the two have been found produce similar results in the cases analyzed. We ask whether or not Boolean models can generically reproduce the qualitative attractor dynamics of networks of continuously valued elements. Using a combination of analytical techniques and numerical simulations, we find that continuous networks exhibit two effects---an asymmetry between on and off states, and a decaying memory of events in each element's inputs---that are absent from synchronously updated Boolean models. We show that in simple loops these effects produce exactly the attractors that one would predict with an analysis of the stability of Boolean attractors, but in slightly more complicated topologies, they can destabilize solutions that are stable in the Boolean approximation, and can stabilize new attractors. Second, we investigate ensembles of large, random networks. Of particular interest is the transition between ordered and disordered dynamics, which is well characterized in Boolean systems. Networks at the transition point, called critical, exhibit many of the features of regulatory networks, and recent studies suggest that some specific regulatory networks are indeed near-critical. We ask whether certain statistical measures of the ensemble behavior of large continuous networks are reproduced by Boolean models. We find that, in spite of the lack of correspondence between attractors observed in smaller systems, the statistical characterization given by the continuous and Boolean models show close agreement, and the transition between order and disorder known in Boolean systems can occur in continuous systems as well. One effect that is not present in Boolean systems, the failure of information to propagate down chains of elements of arbitrary length, is present in a class of continuous networks. In these systems, a modified Boolean theory that takes into account the collective effect of propagation failure on chains throughout the network gives a good description of the observed behavior. We find that propagation failure pushes the system toward greater order, resulting in a partial or complete suppression of the disordered phase. Finally, we explore a dynamical process of direct biological relevance: asymmetric cell division in A. thaliana. The long term goal is to develop a model for the process that accurately accounts for both wild type and mutant behavior. To contribute to this endeavor, we use confocal microscopy to image roots in a SHORT-ROOT inducible mutant. We compute correlation functions between the locations of asymmetrically divided cells, and we construct stochastic models based on a few simple assumptions that accurately predict the non-zero correlations. Our result shows that intracellular processes alone cannot be responsible for the observed divisions, and that an intercell signaling mechanism could account for the measured correlations.

Automatic Screening for Perturbations in Boolean Networks.

PubMed

Schwab, Julian D; Kestler, Hans A

2018-01-01

A common approach to address biological questions in systems biology is to simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used to model the dynamics of regulatory processes in biology. Boolean network models allow simulating the qualitative behavior of the modeled processes. A central objective in the simulation of Boolean networks is the computation of their long-term behavior-so-called attractors. These attractors are of special interest as they can often be linked to biologically relevant behaviors. Changing internal and external conditions can influence the long-term behavior of the Boolean network model. Perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another element can lead to different attractors. Apparently, the number of possible perturbations and combinations of perturbations increases exponentially with the size of the network. Manually screening a set of possible components for combinations that have a desired effect on the long-term behavior can be very time consuming if not impossible. We developed a method to automatically screen for perturbations that lead to a user-specified change in the network's functioning. This method is implemented in the visual simulation framework ViSiBool utilizing satisfiability (SAT) solvers for fast exhaustive attractor search.

An Automated Design Framework for Multicellular Recombinase Logic.

PubMed

Guiziou, Sarah; Ulliana, Federico; Moreau, Violaine; Leclere, Michel; Bonnet, Jerome

2018-05-18

Tools to systematically reprogram cellular behavior are crucial to address pressing challenges in manufacturing, environment, or healthcare. Recombinases can very efficiently encode Boolean and history-dependent logic in many species, yet current designs are performed on a case-by-case basis, limiting their scalability and requiring time-consuming optimization. Here we present an automated workflow for designing recombinase logic devices executing Boolean functions. Our theoretical framework uses a reduced library of computational devices distributed into different cellular subpopulations, which are then composed in various manners to implement all desired logic functions at the multicellular level. Our design platform called CALIN (Composable Asynchronous Logic using Integrase Networks) is broadly accessible via a web server, taking truth tables as inputs and providing corresponding DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin ). We anticipate that this automated design workflow will streamline the implementation of Boolean functions in many organisms and for various applications.

Multilayer neural networks with extensively many hidden units.

PubMed

Rosen-Zvi, M; Engel, A; Kanter, I

2001-08-13

The information processing abilities of a multilayer neural network with a number of hidden units scaling as the input dimension are studied using statistical mechanics methods. The mapping from the input layer to the hidden units is performed by general symmetric Boolean functions, whereas the hidden layer is connected to the output by either discrete or continuous couplings. Introducing an overlap in the space of Boolean functions as order parameter, the storage capacity is found to scale with the logarithm of the number of implementable Boolean functions. The generalization behavior is smooth for continuous couplings and shows a discontinuous transition to perfect generalization for discrete ones.

Evolution of a designless nanoparticle network into reconfigurable Boolean logic

NASA Astrophysics Data System (ADS)

Bose, S. K.; Lawrence, C. P.; Liu, Z.; Makarenko, K. S.; van Damme, R. M. J.; Broersma, H. J.; van der Wiel, W. G.

2015-12-01

Natural computers exploit the emergent properties and massive parallelism of interconnected networks of locally active components. Evolution has resulted in systems that compute quickly and that use energy efficiently, utilizing whatever physical properties are exploitable. Man-made computers, on the other hand, are based on circuits of functional units that follow given design rules. Hence, potentially exploitable physical processes, such as capacitive crosstalk, to solve a problem are left out. Until now, designless nanoscale networks of inanimate matter that exhibit robust computational functionality had not been realized. Here we artificially evolve the electrical properties of a disordered nanomaterials system (by optimizing the values of control voltages using a genetic algorithm) to perform computational tasks reconfigurably. We exploit the rich behaviour that emerges from interconnected metal nanoparticles, which act as strongly nonlinear single-electron transistors, and find that this nanoscale architecture can be configured in situ into any Boolean logic gate. This universal, reconfigurable gate would require about ten transistors in a conventional circuit. Our system meets the criteria for the physical realization of (cellular) neural networks: universality (arbitrary Boolean functions), compactness, robustness and evolvability, which implies scalability to perform more advanced tasks. Our evolutionary approach works around device-to-device variations and the accompanying uncertainties in performance. Moreover, it bears a great potential for more energy-efficient computation, and for solving problems that are very hard to tackle in conventional architectures.

Negative Difference Resistance and Its Application to Construct Boolean Logic Circuits

NASA Astrophysics Data System (ADS)

Nikodem, Maciej; Bawiec, Marek A.; Surmacz, Tomasz R.

Electronic circuits based on nanodevices and quantum effect are the future of logic circuits design. Today's technology allows constructing resonant tunneling diodes, quantum cellular automata and nanowires/nanoribbons that are the elementary components of threshold gates. However, synthesizing a threshold circuit for an arbitrary logic function is still a challenging task where no efficient algorithms exist. This paper focuses on Generalised Threshold Gates (GTG), giving the overview of threshold circuit synthesis methods and presenting an algorithm that considerably simplifies the task in case of GTG circuits.

Experimental Clocking of Nanomagnets with Strain for Ultralow Power Boolean Logic.

PubMed

D'Souza, Noel; Salehi Fashami, Mohammad; Bandyopadhyay, Supriyo; Atulasimha, Jayasimha

2016-02-10

Nanomagnetic implementations of Boolean logic have attracted attention because of their nonvolatility and the potential for unprecedented overall energy-efficiency. Unfortunately, the large dissipative losses that occur when nanomagnets are switched with a magnetic field or spin-transfer-torque severely compromise the energy-efficiency. Recently, there have been experimental reports of utilizing the Spin Hall effect for switching magnets, and theoretical proposals for strain induced switching of single-domain magnetostrictive nanomagnets, that might reduce the dissipative losses significantly. Here, we experimentally demonstrate, for the first time that strain-induced switching of single-domain magnetostrictive nanomagnets of lateral dimensions ∼200 nm fabricated on a piezoelectric substrate can implement a nanomagnetic Boolean NOT gate and steer bit information unidirectionally in dipole-coupled nanomagnet chains. On the basis of the experimental results with bulk PMN-PT substrates, we estimate that the energy dissipation for logic operations in a reasonably scaled system using thin films will be a mere ∼1 aJ/bit.

Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction.

PubMed

Velderraín, José Dávila; Martínez-García, Juan Carlos; Álvarez-Buylla, Elena R

2017-01-01

Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.

Reprogrammable logic in memristive crossbar for in-memory computing

NASA Astrophysics Data System (ADS)

Cheng, Long; Zhang, Mei-Yun; Li, Yi; Zhou, Ya-Xiong; Wang, Zhuo-Rui; Hu, Si-Yu; Long, Shi-Bing; Liu, Ming; Miao, Xiang-Shui

2017-12-01

Memristive stateful logic has emerged as a promising next-generation in-memory computing paradigm to address escalating computing-performance pressures in traditional von Neumann architecture. Here, we present a nonvolatile reprogrammable logic method that can process data between different rows and columns in a memristive crossbar array based on material implication (IMP) logic. Arbitrary Boolean logic can be executed with a reprogrammable cell containing four memristors in a crossbar array. In the fabricated Ti/HfO2/W memristive array, some fundamental functions, such as universal NAND logic and data transfer, were experimentally implemented. Moreover, using eight memristors in a 2  ×  4 array, a one-bit full adder was theoretically designed and verified by simulation to exhibit the feasibility of our method to accomplish complex computing tasks. In addition, some critical logic-related performances were further discussed, such as the flexibility of data processing, cascading problem and bit error rate. Such a method could be a step forward in developing IMP-based memristive nonvolatile logic for large-scale in-memory computing architecture.

A sparse matrix algorithm on the Boolean vector machine

NASA Technical Reports Server (NTRS)

Wagner, Robert A.; Patrick, Merrell L.

1988-01-01

VLSI technology is being used to implement a prototype Boolean Vector Machine (BVM), which is a large network of very small processors with equally small memories that operate in SIMD mode; these use bit-serial arithmetic, and communicate via cube-connected cycles network. The BVM's bit-serial arithmetic and the small memories of individual processors are noted to compromise the system's effectiveness in large numerical problem applications. Attention is presently given to the implementation of a basic matrix-vector iteration algorithm for space matrices of the BVM, in order to generate over 1 billion useful floating-point operations/sec for this iteration algorithm. The algorithm is expressed in a novel language designated 'BVM'.

A procedure concept for local reflex control of grasping

NASA Technical Reports Server (NTRS)

Fiorini, Paolo; Chang, Jeffrey

1989-01-01

An architecture is proposed for the control of robotic devices, and in particular of anthropomorphic hands, characterized by a hierarchical structure in which every level of the architecture contains data and control function with varying degree of abstraction. Bottom levels of the hierarchy interface directly with sensors and actuators, and process raw data and motor commands. Higher levels perform more symbolic types of tasks, such as application of boolean rules and general planning operations. Layers implementation has to be consistent with the type of operation and its requirements for real time control. It is proposed to implement the rule level with a Boolean Artificial Neural Network characterized by a response time sufficient for producing reflex corrective action at the actuator level.

Autonomous Modeling, Statistical Complexity and Semi-annealed Treatment of Boolean Networks

NASA Astrophysics Data System (ADS)

Gong, Xinwei

This dissertation presents three studies on Boolean networks. Boolean networks are a class of mathematical systems consisting of interacting elements with binary state variables. Each element is a node with a Boolean logic gate, and the presence of interactions between any two nodes is represented by directed links. Boolean networks that implement the logic structures of real systems are studied as coarse-grained models of the real systems. Large random Boolean networks are studied with mean field approximations and used to provide a baseline of possible behaviors of large real systems. This dissertation presents one study of the former type, concerning the stable oscillation of a yeast cell-cycle oscillator, and two studies of the latter type, respectively concerning the statistical complexity of large random Boolean networks and an extension of traditional mean field techniques that accounts for the presence of short loops. In the cell-cycle oscillator study, a novel autonomous update scheme is introduced to study the stability of oscillations in small networks. A motif that corrects pulse-growing perturbations and a motif that grows pulses are identified. A combination of the two motifs is capable of sustaining stable oscillations. Examining a Boolean model of the yeast cell-cycle oscillator using an autonomous update scheme yields evidence that it is endowed with such a combination. Random Boolean networks are classified as ordered, critical or disordered based on their response to small perturbations. In the second study, random Boolean networks are taken as prototypical cases for the evaluation of two measures of complexity based on a criterion for optimal statistical prediction. One measure, defined for homogeneous systems, does not distinguish between the static spatial inhomogeneity in the ordered phase and the dynamical inhomogeneity in the disordered phase. A modification in which complexities of individual nodes are calculated yields vanishing complexity values for networks in the ordered and critical phases and for highly disordered networks, peaking somewhere in the disordered phase. Individual nodes with high complexity have, on average, a larger influence on the system dynamics. Lastly, a semi-annealed approximation that preserves the correlation between states at neighboring nodes is introduced to study a social game-inspired network model in which all links are bidirectional and all nodes have a self-input. The technique developed here is shown to yield accurate predictions of distribution of players' states, and accounts for some nontrivial collective behavior of game theoretic interest.

Boolean logic tree of graphene-based chemical system for molecular computation and intelligent molecular search query.

PubMed

Huang, Wei Tao; Luo, Hong Qun; Li, Nian Bing

2014-05-06

The most serious, and yet unsolved, problem of constructing molecular computing devices consists in connecting all of these molecular events into a usable device. This report demonstrates the use of Boolean logic tree for analyzing the chemical event network based on graphene, organic dye, thrombin aptamer, and Fenton reaction, organizing and connecting these basic chemical events. And this chemical event network can be utilized to implement fluorescent combinatorial logic (including basic logic gates and complex integrated logic circuits) and fuzzy logic computing. On the basis of the Boolean logic tree analysis and logic computing, these basic chemical events can be considered as programmable "words" and chemical interactions as "syntax" logic rules to construct molecular search engine for performing intelligent molecular search query. Our approach is helpful in developing the advanced logic program based on molecules for application in biosensing, nanotechnology, and drug delivery.

Toward using games to teach fundamental computer science concepts

NASA Astrophysics Data System (ADS)

Edgington, Jeffrey Michael

Video and computer games have become an important area of study in the field of education. Games have been designed to teach mathematics, physics, raise social awareness, teach history and geography, and train soldiers in the military. Recent work has created computer games for teaching computer programming and understanding basic algorithms. We present an investigation where computer games are used to teach two fundamental computer science concepts: boolean expressions and recursion. The games are intended to teach the concepts and not how to implement them in a programming language. For this investigation, two computer games were created. One is designed to teach basic boolean expressions and operators and the other to teach fundamental concepts of recursion. We describe the design and implementation of both games. We evaluate the effectiveness of these games using before and after surveys. The surveys were designed to ascertain basic understanding, attitudes and beliefs regarding the concepts. The boolean game was evaluated with local high school students and students in a college level introductory computer science course. The recursion game was evaluated with students in a college level introductory computer science course. We present the analysis of the collected survey information for both games. This analysis shows a significant positive change in student attitude towards recursion and modest gains in student learning outcomes for both topics.

PyBoolNet: a python package for the generation, analysis and visualization of boolean networks.

PubMed

Klarner, Hannes; Streck, Adam; Siebert, Heike

2017-03-01

The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts. P y B ool N et is a Python package for working with Boolean networks that supports simple access to model checking via N u SMV, standard graph algorithms via N etwork X and visualization via dot . In addition, state of the art attractor computation exploiting P otassco ASP is implemented. The package is function-based and uses only native Python and N etwork X data types. https://github.com/hklarner/PyBoolNet. hannes.klarner@fu-berlin.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Nonvolatile reconfigurable sequential logic in a HfO2 resistive random access memory array.

PubMed

Zhou, Ya-Xiong; Li, Yi; Su, Yu-Ting; Wang, Zhuo-Rui; Shih, Ling-Yi; Chang, Ting-Chang; Chang, Kuan-Chang; Long, Shi-Bing; Sze, Simon M; Miao, Xiang-Shui

2017-05-25

Resistive random access memory (RRAM) based reconfigurable logic provides a temporal programmable dimension to realize Boolean logic functions and is regarded as a promising route to build non-von Neumann computing architecture. In this work, a reconfigurable operation method is proposed to perform nonvolatile sequential logic in a HfO 2 -based RRAM array. Eight kinds of Boolean logic functions can be implemented within the same hardware fabrics. During the logic computing processes, the RRAM devices in an array are flexibly configured in a bipolar or complementary structure. The validity was demonstrated by experimentally implemented NAND and XOR logic functions and a theoretically designed 1-bit full adder. With the trade-off between temporal and spatial computing complexity, our method makes better use of limited computing resources, thus provides an attractive scheme for the construction of logic-in-memory systems.

Joint remote control of an arbitrary single-qubit state by using a multiparticle entangled state as the quantum channel

NASA Astrophysics Data System (ADS)

Lv, Shu-Xin; Zhao, Zheng-Wei; Zhou, Ping

2018-01-01

We present a scheme for joint remote implementation of an arbitrary single-qubit operation following some ideas in one-way quantum computation. All the senders share the information of implemented quantum operation and perform corresponding single-qubit measurements according to their information of implemented operation. An arbitrary single-qubit operation can be implemented upon the remote receiver's quantum system if the receiver cooperates with all the senders. Moreover, we study the protocol of multiparty joint remote implementation of an arbitrary single-qubit operation with many senders by using a multiparticle entangled state as the quantum channel.

Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level

NASA Astrophysics Data System (ADS)

Thakar, Juilee; Albert, Réka

The following sections are included: * Introduction * Boolean Network Concepts and History * Extensions of the Classical Boolean Framework * Boolean Inference Methods and Examples in Biology * Dynamic Boolean Models: Examples in Plant Biology, Developmental Biology and Immunology * Conclusions * References

Binary space partitioning trees and their uses

NASA Technical Reports Server (NTRS)

Bell, Bradley N.

1989-01-01

Binary Space Partitioning (BSP) trees have some qualities that make them useful in solving many graphics related problems. The purpose is to describe what a BSP tree is, and how it can be used to solve the problem of hidden surface removal, and constructive solid geometry. The BSP tree is based on the idea that a plane acting as a divider subdivides space into two parts with one being on the positive side and the other on the negative. A polygonal solid is then represented as the volume defined by the collective interior half spaces of the solid's bounding surfaces. The nature of how the tree is organized lends itself well for sorting polygons relative to an arbitrary point in 3 space. The speed at which the tree can be traversed for depth sorting is fast enough to provide hidden surface removal at interactive speeds. The fact that a BSP tree actually represents a polygonal solid as a bounded volume also makes it quite useful in performing the boolean operations used in constructive solid geometry. Due to the nature of the BSP tree, polygons can be classified as they are subdivided. The ability to classify polygons as they are subdivided can enhance the simplicity of implementing constructive solid geometry.

Adaptive Neuro-Fuzzy Determination of the Effect of Experimental Parameters on Vehicle Agent Speed Relative to Vehicle Intruder.

PubMed

Shamshirband, Shahaboddin; Banjanovic-Mehmedovic, Lejla; Bosankic, Ivan; Kasapovic, Suad; Abdul Wahab, Ainuddin Wahid Bin

2016-01-01

Intelligent Transportation Systems rely on understanding, predicting and affecting the interactions between vehicles. The goal of this paper is to choose a small subset from the larger set so that the resulting regression model is simple, yet have good predictive ability for Vehicle agent speed relative to Vehicle intruder. The method of ANFIS (adaptive neuro fuzzy inference system) was applied to the data resulting from these measurements. The ANFIS process for variable selection was implemented in order to detect the predominant variables affecting the prediction of agent speed relative to intruder. This process includes several ways to discover a subset of the total set of recorded parameters, showing good predictive capability. The ANFIS network was used to perform a variable search. Then, it was used to determine how 9 parameters (Intruder Front sensors active (boolean), Intruder Rear sensors active (boolean), Agent Front sensors active (boolean), Agent Rear sensors active (boolean), RSSI signal intensity/strength (integer), Elapsed time (in seconds), Distance between Agent and Intruder (m), Angle of Agent relative to Intruder (angle between vehicles °), Altitude difference between Agent and Intruder (m)) influence prediction of agent speed relative to intruder. The results indicated that distance between Vehicle agent and Vehicle intruder (m) and angle of Vehicle agent relative to Vehicle Intruder (angle between vehicles °) is the most influential parameters to Vehicle agent speed relative to Vehicle intruder.

Nonvolatile “AND,” “OR,” and “NOT” Boolean logic gates based on phase-change memory

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

Li, Y.; Zhong, Y. P.; Deng, Y. F.

2013-12-21

Electronic devices or circuits that can implement both logic and memory functions are regarded as the building blocks for future massive parallel computing beyond von Neumann architecture. Here we proposed phase-change memory (PCM)-based nonvolatile logic gates capable of AND, OR, and NOT Boolean logic operations verified in SPICE simulations and circuit experiments. The logic operations are parallel computing and results can be stored directly in the states of the logic gates, facilitating the combination of computing and memory in the same circuit. These results are encouraging for ultralow-power and high-speed nonvolatile logic circuit design based on novel memory devices.

The Boolean Is Dead, Long Live the Boolean! Natural Language versus Boolean Searching in Introductory Undergraduate Instruction

ERIC Educational Resources Information Center

Lowe, M. Sara; Maxson, Bronwen K.; Stone, Sean M.; Miller, Willie; Snajdr, Eric; Hanna, Kathleen

2018-01-01

Boolean logic can be a difficult concept for first-year, introductory students to grasp. This paper compares the results of Boolean and natural language searching across several databases with searches created from student research questions. Performance differences between databases varied. Overall, natural search language is at least as good as…

Logic circuits from zero forcing.

PubMed

Burgarth, Daniel; Giovannetti, Vittorio; Hogben, Leslie; Severini, Simone; Young, Michael

We design logic circuits based on the notion of zero forcing on graphs; each gate of the circuits is a gadget in which zero forcing is performed. We show that such circuits can evaluate every monotone Boolean function. By using two vertices to encode each logical bit, we obtain universal computation. We also highlight a phenomenon of "back forcing" as a property of each function. Such a phenomenon occurs in a circuit when the input of gates which have been already used at a given time step is further modified by a computation actually performed at a later stage. Finally, we show that zero forcing can be also used to implement reversible computation. The model introduced here provides a potentially new tool in the analysis of Boolean functions, with particular attention to monotonicity. Moreover, in the light of applications of zero forcing in quantum mechanics, the link with Boolean functions may suggest a new directions in quantum control theory and in the study of engineered quantum spin systems. It is an open technical problem to verify whether there is a link between zero forcing and computation with contact circuits.

Boolean dynamics of genetic regulatory networks inferred from microarray time series data

DOE PAGES

Martin, Shawn; Zhang, Zhaoduo; Martino, Anthony; ...

2007-01-31

Methods available for the inference of genetic regulatory networks strive to produce a single network, usually by optimizing some quantity to fit the experimental observations. In this paper we investigate the possibility that multiple networks can be inferred, all resulting in similar dynamics. This idea is motivated by theoretical work which suggests that biological networks are robust and adaptable to change, and that the overall behavior of a genetic regulatory network might be captured in terms of dynamical basins of attraction. We have developed and implemented a method for inferring genetic regulatory networks for time series microarray data. Our methodmore » first clusters and discretizes the gene expression data using k-means and support vector regression. We then enumerate Boolean activation–inhibition networks to match the discretized data. In conclusion, the dynamics of the Boolean networks are examined. We have tested our method on two immunology microarray datasets: an IL-2-stimulated T cell response dataset and a LPS-stimulated macrophage response dataset. In both cases, we discovered that many networks matched the data, and that most of these networks had similar dynamics.« less

Computational complexity of Boolean functions

NASA Astrophysics Data System (ADS)

Korshunov, Aleksei D.

2012-02-01

Boolean functions are among the fundamental objects of discrete mathematics, especially in those of its subdisciplines which fall under mathematical logic and mathematical cybernetics. The language of Boolean functions is convenient for describing the operation of many discrete systems such as contact networks, Boolean circuits, branching programs, and some others. An important parameter of discrete systems of this kind is their complexity. This characteristic has been actively investigated starting from Shannon's works. There is a large body of scientific literature presenting many fundamental results. The purpose of this survey is to give an account of the main results over the last sixty years related to the complexity of computation (realization) of Boolean functions by contact networks, Boolean circuits, and Boolean circuits without branching. Bibliography: 165 titles.

Arbitrary nonlinearity is sufficient to represent all functions by neural networks - A theorem

NASA Technical Reports Server (NTRS)

Kreinovich, Vladik YA.

1991-01-01

It is proved that if we have neurons implementing arbitrary linear functions and a neuron implementing one (arbitrary but smooth) nonlinear function g(x), then for every continuous function f(x sub 1,..., x sub m) of arbitrarily many variables, and for arbitrary e above 0, we can construct a network that consists of g-neurons and linear neurons, and computes f with precision e.

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

PubMed Central

Kerkhofs, Johan; Geris, Liesbet

2015-01-01

Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic quantitative and a limited time resolution to a discrete (Boolean) framework. Quantitative resolution is improved through the employ of normalized variables in unison with an additive approach. Increased time resolution stems from the introduction of two distinct priority classes. Through the implementation of a previously published chondrocyte network and T helper cell network, we show that this addition of quantitative and time resolution broadens the scope of biological behaviour that can be captured by the models. Specifically, the quantitative resolution readily allows models to discern qualitative differences in dosage response to growth factors. The limited time resolution, in turn, can influence the reachability of attractors, delineating the likely long term system behaviour. Importantly, the information required for implementation of these features, such as the nature of an interaction, is typically obtainable from the literature. Nonetheless, a trade-off is always present between additional computational cost of this approach and the likelihood of extending the model’s scope. Indeed, in some cases the inclusion of these features does not yield additional insight. This framework, incorporating increased and readily available time and semi-quantitative resolution, can help in substantiating the litmus test of dynamics for gene networks, firstly by excluding unlikely dynamics and secondly by refining falsifiable predictions on qualitative behaviour. PMID:26067297

Fuzzy expert systems using CLIPS

NASA Technical Reports Server (NTRS)

Le, Thach C.

1994-01-01

This paper describes a CLIPS-based fuzzy expert system development environment called FCLIPS and illustrates its application to the simulated cart-pole balancing problem. FCLIPS is a straightforward extension of CLIPS without any alteration to the CLIPS internal structures. It makes use of the object-oriented and module features in CLIPS version 6.0 for the implementation of fuzzy logic concepts. Systems of varying degrees of mixed Boolean and fuzzy rules can be implemented in CLIPS. Design and implementation issues of FCLIPS will also be discussed.

Massive Query Resolution for Rapid Selective Dissemination of Information.

ERIC Educational Resources Information Center

Cohen, Jonathan D.

1999-01-01

Outlines an efficient approach to performing query resolution which, when matched with a keyword scanner, offers rapid selecting and routing for massive Boolean queries, and which is suitable for implementation on a desktop computer. Demonstrates the system's operation with large examples in a practical setting. (AEF)

Cryptographic Boolean Functions with Biased Inputs

DTIC Science & Technology

2015-07-31

theory of random graphs developed by Erdős and Rényi [2]. The graph properties in a random graph expressed as such Boolean functions are used by...distributed Bernoulli variates with the parameter p. Since our scope is within the area of cryptography , we initiate an analysis of cryptographic...Boolean functions with biased inputs, which we refer to as µp-Boolean functions, is a common generalization of Boolean functions which stems from the

Evolutionary Algorithms for Boolean Functions in Diverse Domains of Cryptography.

PubMed

Picek, Stjepan; Carlet, Claude; Guilley, Sylvain; Miller, Julian F; Jakobovic, Domagoj

2016-01-01

The role of Boolean functions is prominent in several areas including cryptography, sequences, and coding theory. Therefore, various methods for the construction of Boolean functions with desired properties are of direct interest. New motivations on the role of Boolean functions in cryptography with attendant new properties have emerged over the years. There are still many combinations of design criteria left unexplored and in this matter evolutionary computation can play a distinct role. This article concentrates on two scenarios for the use of Boolean functions in cryptography. The first uses Boolean functions as the source of the nonlinearity in filter and combiner generators. Although relatively well explored using evolutionary algorithms, it still presents an interesting goal in terms of the practical sizes of Boolean functions. The second scenario appeared rather recently where the objective is to find Boolean functions that have various orders of the correlation immunity and minimal Hamming weight. In both these scenarios we see that evolutionary algorithms are able to find high-quality solutions where genetic programming performs the best.

3D GIS spatial operation based on extended Euler operators

NASA Astrophysics Data System (ADS)

Xu, Hongbo; Lu, Guonian; Sheng, Yehua; Zhou, Liangchen; Guo, Fei; Shang, Zuoyan; Wang, Jing

2008-10-01

The implementation of 3 dimensions spatial operations, based on certain data structure, has a lack of universality and is not able to treat with non-manifold cases, at present. ISO/DIS 19107 standard just presents the definition of Boolean operators and set operators for topological relationship query, and OGC GeoXACML gives formal definitions for several set functions without implementation detail. Aiming at these problems, based mathematical foundation on cell complex theory, supported by non-manifold data structure and using relevant research in the field of non-manifold geometry modeling for reference, firstly, this paper according to non-manifold Euler-Poincaré formula constructs 6 extended Euler operators and inverse operators to carry out creating, updating and deleting 3D spatial elements, as well as several pairs of supplementary Euler operators to convenient for implementing advanced functions. Secondly, we change topological element operation sequence of Boolean operation and set operation as well as set functions defined in GeoXACML into combination of extended Euler operators, which separates the upper functions and lower data structure. Lastly, we develop underground 3D GIS prototype system, in which practicability and credibility of extended Euler operators faced to 3D GIS presented by this paper are validated.

A Simple Blueprint for Automatic Boolean Query Processing.

ERIC Educational Resources Information Center

Salton, G.

1988-01-01

Describes a new Boolean retrieval environment in which an extended soft Boolean logic is used to automatically construct queries from original natural language formulations provided by users. Experimental results that compare the retrieval effectiveness of this method to conventional Boolean and vector processing are discussed. (27 references)…

Optimal stabilization of Boolean networks through collective influence

NASA Astrophysics Data System (ADS)

Wang, Jiannan; Pei, Sen; Wei, Wei; Feng, Xiangnan; Zheng, Zhiming

2018-03-01

Boolean networks have attracted much attention due to their wide applications in describing dynamics of biological systems. During past decades, much effort has been invested in unveiling how network structure and update rules affect the stability of Boolean networks. In this paper, we aim to identify and control a minimal set of influential nodes that is capable of stabilizing an unstable Boolean network. For locally treelike Boolean networks with biased truth tables, we propose a greedy algorithm to identify influential nodes in Boolean networks by minimizing the largest eigenvalue of a modified nonbacktracking matrix. We test the performance of the proposed collective influence algorithm on four different networks. Results show that the collective influence algorithm can stabilize each network with a smaller set of nodes compared with other heuristic algorithms. Our work provides a new insight into the mechanism that determines the stability of Boolean networks, which may find applications in identifying virulence genes that lead to serious diseases.

Effect of memory in non-Markovian Boolean networks illustrated with a case study: A cell cycling process

NASA Astrophysics Data System (ADS)

Ebadi, H.; Saeedian, M.; Ausloos, M.; Jafari, G. R.

2016-11-01

The Boolean network is one successful model to investigate discrete complex systems such as the gene interacting phenomenon. The dynamics of a Boolean network, controlled with Boolean functions, is usually considered to be a Markovian (memory-less) process. However, both self-organizing features of biological phenomena and their intelligent nature should raise some doubt about ignoring the history of their time evolution. Here, we extend the Boolean network Markovian approach: we involve the effect of memory on the dynamics. This can be explored by modifying Boolean functions into non-Markovian functions, for example, by investigating the usual non-Markovian threshold function —one of the most applied Boolean functions. By applying the non-Markovian threshold function on the dynamical process of the yeast cell cycle network, we discover a power-law-like memory with a more robust dynamics than the Markovian dynamics.

Mining TCGA Data Using Boolean Implications

PubMed Central

Sinha, Subarna; Tsang, Emily K.; Zeng, Haoyang; Meister, Michela; Dill, David L.

2014-01-01

Boolean implications (if-then rules) provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression) from the glioblastoma (GBM) and ovarian serous cystadenoma (OV) data sets from The Cancer Genome Atlas (TCGA). We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/. PMID:25054200

Integrated-Circuit Pseudorandom-Number Generator

NASA Technical Reports Server (NTRS)

Steelman, James E.; Beasley, Jeff; Aragon, Michael; Ramirez, Francisco; Summers, Kenneth L.; Knoebel, Arthur

1992-01-01

Integrated circuit produces 8-bit pseudorandom numbers from specified probability distribution, at rate of 10 MHz. Use of Boolean logic, circuit implements pseudorandom-number-generating algorithm. Circuit includes eight 12-bit pseudorandom-number generators, outputs are uniformly distributed. 8-bit pseudorandom numbers satisfying specified nonuniform probability distribution are generated by processing uniformly distributed outputs of eight 12-bit pseudorandom-number generators through "pipeline" of D flip-flops, comparators, and memories implementing conditional probabilities on zeros and ones.

Design of a Nanoscale, CMOS-Integrable, Thermal-Guiding Structure for Boolean-Logic and Neuromorphic Computation.

PubMed

Loke, Desmond; Skelton, Jonathan M; Chong, Tow-Chong; Elliott, Stephen R

2016-12-21

One of the requirements for achieving faster CMOS electronics is to mitigate the unacceptably large chip areas required to steer heat away from or, more recently, toward the critical nodes of state-of-the-art devices. Thermal-guiding (TG) structures can efficiently direct heat by "meta-materials" engineering; however, some key aspects of the behavior of these systems are not fully understood. Here, we demonstrate control of the thermal-diffusion properties of TG structures by using nanometer-scale, CMOS-integrable, graphene-on-silica stacked materials through finite-element-methods simulations. It has been shown that it is possible to implement novel, controllable, thermally based Boolean-logic and spike-timing-dependent plasticity operations for advanced (neuromorphic) computing applications using such thermal-guide architectures.

Synchronization of coupled large-scale Boolean networks

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

Li, Fangfei, E-mail: li-fangfei@163.com

2014-03-15

This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.

State feedback controller design for the synchronization of Boolean networks with time delays

NASA Astrophysics Data System (ADS)

Li, Fangfei; Li, Jianning; Shen, Lijuan

2018-01-01

State feedback control design to make the response Boolean network synchronize with the drive Boolean network is far from being solved in the literature. Motivated by this, this paper studies the feedback control design for the complete synchronization of two coupled Boolean networks with time delays. A necessary condition for the existence of a state feedback controller is derived first. Then the feedback control design procedure for the complete synchronization of two coupled Boolean networks is provided based on the necessary condition. Finally, an example is given to illustrate the proposed design procedure.

The mathematics of a quantum Hamiltonian computing half adder Boolean logic gate.

PubMed

Dridi, G; Julien, R; Hliwa, M; Joachim, C

2015-08-28

The mathematics behind the quantum Hamiltonian computing (QHC) approach of designing Boolean logic gates with a quantum system are given. Using the quantum eigenvalue repulsion effect, the QHC AND, NAND, OR, NOR, XOR, and NXOR Hamiltonian Boolean matrices are constructed. This is applied to the construction of a QHC half adder Hamiltonian matrix requiring only six quantum states to fullfil a half Boolean logical truth table. The QHC design rules open a nano-architectronic way of constructing Boolean logic gates inside a single molecule or atom by atom at the surface of a passivated semi-conductor.

Development of Boolean calculus and its application

NASA Technical Reports Server (NTRS)

Tapia, M. A.

1979-01-01

Formal procedures for synthesis of asynchronous sequential system using commercially available edge-sensitive flip-flops are developed. Boolean differential is defined. The exact number of compatible integrals of a Boolean differential were calculated.

Boolean integral calculus

NASA Technical Reports Server (NTRS)

Tucker, Jerry H.; Tapia, Moiez A.; Bennett, A. Wayne

1988-01-01

The concept of Boolean integration is developed, and different Boolean integral operators are introduced. Given the changes in a desired function in terms of the changes in its arguments, the ways of 'integrating' (i.e. realizing) such a function, if it exists, are presented. The necessary and sufficient conditions for integrating, in different senses, the expression specifying the changes are obtained. Boolean calculus has applications in the design of logic circuits and in fault analysis.

Modeling the Normal and Neoplastic Cell Cycle with 'Realistic Boolean Genetic Networks': Their Application for Understanding Carcinogenesis and Assessing Therapeutic Strategies

NASA Technical Reports Server (NTRS)

Szallasi, Zoltan; Liang, Shoudan

2000-01-01

In this paper we show how Boolean genetic networks could be used to address complex problems in cancer biology. First, we describe a general strategy to generate Boolean genetic networks that incorporate all relevant biochemical and physiological parameters and cover all of their regulatory interactions in a deterministic manner. Second, we introduce 'realistic Boolean genetic networks' that produce time series measurements very similar to those detected in actual biological systems. Third, we outline a series of essential questions related to cancer biology and cancer therapy that could be addressed by the use of 'realistic Boolean genetic network' modeling.

Automatic query formulations in information retrieval.

PubMed

Salton, G; Buckley, C; Fox, E A

1983-07-01

Modern information retrieval systems are designed to supply relevant information in response to requests received from the user population. In most retrieval environments the search requests consist of keywords, or index terms, interrelated by appropriate Boolean operators. Since it is difficult for untrained users to generate effective Boolean search requests, trained search intermediaries are normally used to translate original statements of user need into useful Boolean search formulations. Methods are introduced in this study which reduce the role of the search intermediaries by making it possible to generate Boolean search formulations completely automatically from natural language statements provided by the system patrons. Frequency considerations are used automatically to generate appropriate term combinations as well as Boolean connectives relating the terms. Methods are covered to produce automatic query formulations both in a standard Boolean logic system, as well as in an extended Boolean system in which the strict interpretation of the connectives is relaxed. Experimental results are supplied to evaluate the effectiveness of the automatic query formulation process, and methods are described for applying the automatic query formulation process in practice.

An Attractor-Based Complexity Measurement for Boolean Recurrent Neural Networks

PubMed Central

Cabessa, Jérémie; Villa, Alessandro E. P.

2014-01-01

We provide a novel refined attractor-based complexity measurement for Boolean recurrent neural networks that represents an assessment of their computational power in terms of the significance of their attractor dynamics. This complexity measurement is achieved by first proving a computational equivalence between Boolean recurrent neural networks and some specific class of -automata, and then translating the most refined classification of -automata to the Boolean neural network context. As a result, a hierarchical classification of Boolean neural networks based on their attractive dynamics is obtained, thus providing a novel refined attractor-based complexity measurement for Boolean recurrent neural networks. These results provide new theoretical insights to the computational and dynamical capabilities of neural networks according to their attractive potentialities. An application of our findings is illustrated by the analysis of the dynamics of a simplified model of the basal ganglia-thalamocortical network simulated by a Boolean recurrent neural network. This example shows the significance of measuring network complexity, and how our results bear new founding elements for the understanding of the complexity of real brain circuits. PMID:24727866

Proposed method to construct Boolean functions with maximum possible annihilator immunity

NASA Astrophysics Data System (ADS)

Goyal, Rajni; Panigrahi, Anupama; Bansal, Rohit

2017-07-01

Nonlinearity and Algebraic(annihilator) immunity are two core properties of a Boolean function because optimum values of Annihilator Immunity and nonlinearity are required to resist fast algebraic attack and differential cryptanalysis respectively. For a secure cypher system, Boolean function(S-Boxes) should resist maximum number of attacks. It is possible if a Boolean function has optimal trade-off among its properties. Before constructing Boolean functions, we fixed the criteria of our constructions based on its properties. In present work, our construction is based on annihilator immunity and nonlinearity. While keeping above facts in mind,, we have developed a multi-objective evolutionary approach based on NSGA-II and got the optimum value of annihilator immunity with good bound of nonlinearity. We have constructed balanced Boolean functions having the best trade-off among balancedness, Annihilator immunity and nonlinearity for 5, 6 and 7 variables by the proposed method.

Compile-Time Schedulability Analysis of Communicating Concurrent Programs

DTIC Science & Technology

2006-06-28

synchronize via the read and write operations on the FIFO channels. These operations have been implemented with the help of semaphores , which...3 1.1.2 Synchronous Dataflow . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.1.3 Boolean Dataflow...described by concurrent programs . . . . . . . . . 4 1.3 A synchronous dataflow model, its topology matrix, and repetition vector . 10 1.4 Select and

Passive dendrites enable single neurons to compute linearly non-separable functions.

PubMed

Cazé, Romain Daniel; Humphries, Mark; Gutkin, Boris

2013-01-01

Local supra-linear summation of excitatory inputs occurring in pyramidal cell dendrites, the so-called dendritic spikes, results in independent spiking dendritic sub-units, which turn pyramidal neurons into two-layer neural networks capable of computing linearly non-separable functions, such as the exclusive OR. Other neuron classes, such as interneurons, may possess only a few independent dendritic sub-units, or only passive dendrites where input summation is purely sub-linear, and where dendritic sub-units are only saturating. To determine if such neurons can also compute linearly non-separable functions, we enumerate, for a given parameter range, the Boolean functions implementable by a binary neuron model with a linear sub-unit and either a single spiking or a saturating dendritic sub-unit. We then analytically generalize these numerical results to an arbitrary number of non-linear sub-units. First, we show that a single non-linear dendritic sub-unit, in addition to the somatic non-linearity, is sufficient to compute linearly non-separable functions. Second, we analytically prove that, with a sufficient number of saturating dendritic sub-units, a neuron can compute all functions computable with purely excitatory inputs. Third, we show that these linearly non-separable functions can be implemented with at least two strategies: one where a dendritic sub-unit is sufficient to trigger a somatic spike; another where somatic spiking requires the cooperation of multiple dendritic sub-units. We formally prove that implementing the latter architecture is possible with both types of dendritic sub-units whereas the former is only possible with spiking dendrites. Finally, we show how linearly non-separable functions can be computed by a generic two-compartment biophysical model and a realistic neuron model of the cerebellar stellate cell interneuron. Taken together our results demonstrate that passive dendrites are sufficient to enable neurons to compute linearly non-separable functions.

Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions

PubMed Central

Cazé, Romain Daniel; Humphries, Mark; Gutkin, Boris

2013-01-01

Local supra-linear summation of excitatory inputs occurring in pyramidal cell dendrites, the so-called dendritic spikes, results in independent spiking dendritic sub-units, which turn pyramidal neurons into two-layer neural networks capable of computing linearly non-separable functions, such as the exclusive OR. Other neuron classes, such as interneurons, may possess only a few independent dendritic sub-units, or only passive dendrites where input summation is purely sub-linear, and where dendritic sub-units are only saturating. To determine if such neurons can also compute linearly non-separable functions, we enumerate, for a given parameter range, the Boolean functions implementable by a binary neuron model with a linear sub-unit and either a single spiking or a saturating dendritic sub-unit. We then analytically generalize these numerical results to an arbitrary number of non-linear sub-units. First, we show that a single non-linear dendritic sub-unit, in addition to the somatic non-linearity, is sufficient to compute linearly non-separable functions. Second, we analytically prove that, with a sufficient number of saturating dendritic sub-units, a neuron can compute all functions computable with purely excitatory inputs. Third, we show that these linearly non-separable functions can be implemented with at least two strategies: one where a dendritic sub-unit is sufficient to trigger a somatic spike; another where somatic spiking requires the cooperation of multiple dendritic sub-units. We formally prove that implementing the latter architecture is possible with both types of dendritic sub-units whereas the former is only possible with spiking dendrites. Finally, we show how linearly non-separable functions can be computed by a generic two-compartment biophysical model and a realistic neuron model of the cerebellar stellate cell interneuron. Taken together our results demonstrate that passive dendrites are sufficient to enable neurons to compute linearly non-separable functions. PMID:23468600

To Boolean or Not To Boolean.

ERIC Educational Resources Information Center

Hildreth, Charles R.

1983-01-01

This editorial addresses the issue of whether or not to provide free-text, keyword/boolean search capabilities in the information retrieval mechanisms of online public access catalogs and discusses online catalogs developed prior to 1980--keyword searching, phrase searching, and precoordination and postcoordination. (EJS)

Minimum energy control and optimal-satisfactory control of Boolean control network

NASA Astrophysics Data System (ADS)

Li, Fangfei; Lu, Xiwen

2013-12-01

In the literatures, to transfer the Boolean control network from the initial state to the desired state, the expenditure of energy has been rarely considered. Motivated by this, this Letter investigates the minimum energy control and optimal-satisfactory control of Boolean control network. Based on the semi-tensor product of matrices and Floyd's algorithm, minimum energy, constrained minimum energy and optimal-satisfactory control design for Boolean control network are given respectively. A numerical example is presented to illustrate the efficiency of the obtained results.

Simultaneous G-Quadruplex DNA Logic.

PubMed

Bader, Antoine; Cockroft, Scott L

2018-04-03

A fundamental principle of digital computer operation is Boolean logic, where inputs and outputs are described by binary integer voltages. Similarly, inputs and outputs may be processed on the molecular level as exemplified by synthetic circuits that exploit the programmability of DNA base-pairing. Unlike modern computers, which execute large numbers of logic gates in parallel, most implementations of molecular logic have been limited to single computing tasks, or sensing applications. This work reports three G-quadruplex-based logic gates that operate simultaneously in a single reaction vessel. The gates respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis. The modular, addressable, and label-free approach could be incorporated into DNA-based sensors, or used for resolving and debugging parallel processes in DNA computing applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A solution to the surface intersection problem. [Boolean functions in geometric modeling

NASA Technical Reports Server (NTRS)

Timer, H. G.

1977-01-01

An application-independent geometric model within a data base framework should support the use of Boolean operators which allow the user to construct a complex model by appropriately combining a series of simple models. The use of these operators leads to the concept of implicitly and explicitly defined surfaces. With an explicitly defined model, the surface area may be computed by simply summing the surface areas of the bounding surfaces. For an implicitly defined model, the surface area computation must deal with active and inactive regions. Because the surface intersection problem involves four unknowns and its solution is a space curve, the parametric coordinates of each surface must be determined as a function of the arc length. Various subproblems involved in the general intersection problem are discussed, and the mathematical basis for their solution is presented along with a program written in FORTRAN IV for implementation on the IBM 370 TSO system.

Identifying a Probabilistic Boolean Threshold Network From Samples.

PubMed

Melkman, Avraham A; Cheng, Xiaoqing; Ching, Wai-Ki; Akutsu, Tatsuya

2018-04-01

This paper studies the problem of exactly identifying the structure of a probabilistic Boolean network (PBN) from a given set of samples, where PBNs are probabilistic extensions of Boolean networks. Cheng et al. studied the problem while focusing on PBNs consisting of pairs of AND/OR functions. This paper considers PBNs consisting of Boolean threshold functions while focusing on those threshold functions that have unit coefficients. The treatment of Boolean threshold functions, and triplets and -tuplets of such functions, necessitates a deepening of the theoretical analyses. It is shown that wide classes of PBNs with such threshold functions can be exactly identified from samples under reasonable constraints, which include: 1) PBNs in which any number of threshold functions can be assigned provided that all have the same number of input variables and 2) PBNs consisting of pairs of threshold functions with different numbers of input variables. It is also shown that the problem of deciding the equivalence of two Boolean threshold functions is solvable in pseudopolynomial time but remains co-NP complete.

Construction of a fuzzy and Boolean logic gates based on DNA.

PubMed

Zadegan, Reza M; Jepsen, Mette D E; Hildebrandt, Lasse L; Birkedal, Victoria; Kjems, Jørgen

2015-04-17

Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridization properties, structure, and function of nucleic acids can be used to make DNA-based logic gates. These devices are important modules in molecular computing and biosensing. The ideal logic gate system should provide a wide selection of logical operations, and be integrable in multiple copies into more complex structures. Here we show the successful construction of a small DNA-based logic gate complex that produces fluorescent outputs corresponding to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three-dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular Networks.

PubMed

Muñoz, Stalin; Carrillo, Miguel; Azpeitia, Eugenio; Rosenblueth, David A

2018-01-01

Boolean networks are important models of biochemical systems, located at the high end of the abstraction spectrum. A number of Boolean gene networks have been inferred following essentially the same method. Such a method first considers experimental data for a typically underdetermined "regulation" graph. Next, Boolean networks are inferred by using biological constraints to narrow the search space, such as a desired set of (fixed-point or cyclic) attractors. We describe Griffin , a computer tool enhancing this method. Griffin incorporates a number of well-established algorithms, such as Dubrova and Teslenko's algorithm for finding attractors in synchronous Boolean networks. In addition, a formal definition of regulation allows Griffin to employ "symbolic" techniques, able to represent both large sets of network states and Boolean constraints. We observe that when the set of attractors is required to be an exact set, prohibiting additional attractors, a naive Boolean coding of this constraint may be unfeasible. Such cases may be intractable even with symbolic methods, as the number of Boolean constraints may be astronomically large. To overcome this problem, we employ an Artificial Intelligence technique known as "clause learning" considerably increasing Griffin 's scalability. Without clause learning only toy examples prohibiting additional attractors are solvable: only one out of seven queries reported here is answered. With clause learning, by contrast, all seven queries are answered. We illustrate Griffin with three case studies drawn from the Arabidopsis thaliana literature. Griffin is available at: http://turing.iimas.unam.mx/griffin.

On the Run-Time Optimization of the Boolean Logic of a Program.

ERIC Educational Resources Information Center

Cadolino, C.; Guazzo, M.

1982-01-01

Considers problem of optimal scheduling of Boolean expression (each Boolean variable represents binary outcome of program module) on single-processor system. Optimization discussed consists of finding operand arrangement that minimizes average execution costs representing consumption of resources (elapsed time, main memory, number of…

Boolean integral calculus for digital systems

NASA Technical Reports Server (NTRS)

Tucker, J. H.; Tapia, M. A.; Bennett, A. W.

1985-01-01

The concept of Boolean integration is introduced and developed. When the changes in a desired function are specified in terms of changes in its arguments, then ways of 'integrating' (i.e., realizing) the function, if it exists, are presented. Boolean integral calculus has applications in design of logic circuits.

Video rate morphological processor based on a redundant number representation

NASA Astrophysics Data System (ADS)

Kuczborski, Wojciech; Attikiouzel, Yianni; Crebbin, Gregory A.

1992-03-01

This paper presents a video rate morphological processor for automated visual inspection of printed circuit boards, integrated circuit masks, and other complex objects. Inspection algorithms are based on gray-scale mathematical morphology. Hardware complexity of the known methods of real-time implementation of gray-scale morphology--the umbra transform and the threshold decomposition--has prompted us to propose a novel technique which applied an arithmetic system without carrying propagation. After considering several arithmetic systems, a redundant number representation has been selected for implementation. Two options are analyzed here. The first is a pure signed digit number representation (SDNR) with the base of 4. The second option is a combination of the base-2 SDNR (to represent gray levels of images) and the conventional twos complement code (to represent gray levels of structuring elements). Operation principle of the morphological processor is based on the concept of the digit level systolic array. Individual processing units and small memory elements create a pipeline. The memory elements store current image windows (kernels). All operation primitives of processing units apply a unified direction of digit processing: most significant digit first (MSDF). The implementation technology is based on the field programmable gate arrays by Xilinx. This paper justified the rationality of a new approach to logic design, which is the decomposition of Boolean functions instead of Boolean minimization.

A Comparison of Two Methods for Boolean Query Relevancy Feedback.

ERIC Educational Resources Information Center

Salton, G.; And Others

1984-01-01

Evaluates and compares two recently proposed automatic methods for relevance feedback of Boolean queries (Dillon method, which uses probabilistic approach as basis, and disjunctive normal form method). Conclusions are drawn concerning the use of effective feedback methods in a Boolean query environment. Nineteen references are included. (EJS)

Modeling and implementation of concurrent logic controllers with use of Petri nets, LSMs, and sequent calculus

NASA Astrophysics Data System (ADS)

Tkacz, J.; Bukowiec, A.; Doligalski, M.

2017-08-01

The paper presentes the method of modeling and implementation of concurrent controllers. Concurrent controllers are specified by Petri nets. Then Petri nets are decomposed using symbolic deduction method of analysis. Formal methods like sequent calculus system with considered elements of Thelen's algorithm have been used here. As a result, linked state machines (LSMs) are received. Each FSM is implemented using methods of structural decomposition during process of logic synthesis. The method of multiple encoding of microinstruction has been applied. It leads to decreased number of Boolean function realized by combinational part of FSM. The additional decoder could be implemented with the use of memory blocks.

Boolean Classes and Qualitative Inquiry. WCER Working Paper No. 2006-3

ERIC Educational Resources Information Center

Nathan, Mitchell J.; Jackson, Kristi

2006-01-01

The prominent role of Boolean classes in qualitative data analysis software is viewed by some as an encroachment of logical positivism on qualitative research methodology. The authors articulate an embodiment perspective, in which Boolean classes are viewed as conceptual metaphors for apprehending and manipulating data, concepts, and categories in…

Algebraic model checking for Boolean gene regulatory networks.

PubMed

Tran, Quoc-Nam

2011-01-01

We present a computational method in which modular and Groebner bases (GB) computation in Boolean rings are used for solving problems in Boolean gene regulatory networks (BN). In contrast to other known algebraic approaches, the degree of intermediate polynomials during the calculation of Groebner bases using our method will never grow resulting in a significant improvement in running time and memory space consumption. We also show how calculation in temporal logic for model checking can be done by means of our direct and efficient Groebner basis computation in Boolean rings. We present our experimental results in finding attractors and control strategies of Boolean networks to illustrate our theoretical arguments. The results are promising. Our algebraic approach is more efficient than the state-of-the-art model checker NuSMV on BNs. More importantly, our approach finds all solutions for the BN problems.

Generalized Flip-Flop Input Equations Based on a Four-Valued Boolean Algebra

NASA Technical Reports Server (NTRS)

Tucker, Jerry H.; Tapia, Moiez A.

1996-01-01

A procedure is developed for obtaining generalized flip-flop input equations, and a concise method is presented for representing these equations. The procedure is based on solving a four-valued characteristic equation of the flip-flop, and can encompass flip-flops that are too complex to approach intuitively. The technique is presented using Karnaugh maps, but could easily be implemented in software.

Spectral methods on arbitrary grids

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.; Gottlieb, David

1995-01-01

Stable and spectrally accurate numerical methods are constructed on arbitrary grids for partial differential equations. These new methods are equivalent to conventional spectral methods but do not rely on specific grid distributions. Specifically, we show how to implement Legendre Galerkin, Legendre collocation, and Laguerre Galerkin methodology on arbitrary grids.

BEAT: A Web-Based Boolean Expression Fault-Based Test Case Generation Tool

ERIC Educational Resources Information Center

Chen, T. Y.; Grant, D. D.; Lau, M. F.; Ng, S. P.; Vasa, V. R.

2006-01-01

BEAT is a Web-based system that generates fault-based test cases from Boolean expressions. It is based on the integration of our several fault-based test case selection strategies. The generated test cases are considered to be fault-based, because they are aiming at the detection of particular faults. For example, when the Boolean expression is in…

On spectral techniques in analysis of Boolean networks

NASA Astrophysics Data System (ADS)

Kesseli, Juha; Rämö, Pauli; Yli-Harja, Olli

2005-06-01

In this work we present results that can be used for analysis of Boolean networks. The results utilize Fourier spectra of the functions in the network. An accurate formula is given for Derrida plots of networks of finite size N based on a result on Boolean functions presented in another context. Derrida plots are widely used to examine the stability issues of Boolean networks. For the limit N→∞, we give a computationally simple form that can be used as a good approximation for rather small networks as well. A formula for Derrida plots of random Boolean networks (RBNs) presented earlier in the literature is given an alternative derivation. It is shown that the information contained in the Derrida plot is equal to the average Fourier spectrum of the functions in the network. In the case of random networks the mean Derrida plot can be obtained from the mean spectrum of the functions. The method is applied to real data by using the Boolean functions found in genetic regulatory networks of eukaryotic cells in an earlier study. Conventionally, Derrida plots and stability analysis have been computed with statistical sampling resulting in poorer accuracy.

Stabilization of perturbed Boolean network attractors through compensatory interactions

PubMed Central

2014-01-01

Background Understanding and ameliorating the effects of network damage are of significant interest, due in part to the variety of applications in which network damage is relevant. For example, the effects of genetic mutations can cascade through within-cell signaling and regulatory networks and alter the behavior of cells, possibly leading to a wide variety of diseases. The typical approach to mitigating network perturbations is to consider the compensatory activation or deactivation of system components. Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade. Results We implement this approach in a Boolean dynamic framework, which has been shown to effectively model the behavior of biological regulatory and signaling networks. We show that the method can stabilize any single state (e.g., fixed point attractors or time-averaged representations of multi-state attractors) to be an attractor of the repaired network. We show that the approach is minimalistic in that few modifications are required to provide stability to a chosen attractor and specific in that interventions do not have undesired effects on the attractor. We apply the approach to random Boolean networks, and further show that the method can in some cases successfully repair synchronous limit cycles. We also apply the methodology to case studies from drought-induced signaling in plants and T-LGL leukemia and find that it is successful in both stabilizing desired behavior and in eliminating undesired outcomes. Code is made freely available through the software package BooleanNet. Conclusions The methodology introduced in this report offers a complementary way to manipulating node expression levels. A comprehensive approach to evaluating network manipulation should take an "all of the above" perspective; we anticipate that theoretical studies of interaction modification, coupled with empirical advances, will ultimately provide researchers with greater flexibility in influencing system behavior. PMID:24885780

The Event Based Language and Its Multiple Processor Implementations.

DTIC Science & Technology

1980-01-01

10 6.1 "Recursive" Linear Fibonacci ................................................ 105 6.2 The Readers Writers Problem...kinds. Examples of such systems are: C.mmp [Wu-72], Pluribus [He-73], Data Flow [ De -75], the boolean n-cube parallel machine [Su-77], and the MuNet [Wa...concurrency within programs; therefore, we hate concentrated on two types of systems which seem suitable: a processor network, and a data flow processor [ De -77

Solving Semantic Searches for Source Code

DTIC Science & Technology

2012-11-01

but of input and expected output pairs. In this domain, those inputs take the form of strings and outputs could be one of sev- eral datatypes ...for some relaxation of CPi that yields C ′ Pi . Encoding weakening is performed by systematically making the constraints on a particular datatype ...the datatypes that can hold concrete or symbolic values: integers, characters, booleans, and strings. The Java implementation uses all the data types

Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines

DTIC Science & Technology

1989-09-01

Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines Srinivas Devadas and Kurt Keutzer F ( Abstract In this...Projects Agency under contract number N00014-87-K-0825. Author Information Devadas : Department of Electrical Engineering and Computer Science, Room 36...MA 02139; (617) 253-0292. 0 * Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines Siivas Devadas

Realisation of all 16 Boolean logic functions in a single magnetoresistance memory cell.

PubMed

Gao, Shuang; Yang, Guang; Cui, Bin; Wang, Shouguo; Zeng, Fei; Song, Cheng; Pan, Feng

2016-07-07

Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future.

All optical logic for optical pattern recognition and networking applications

NASA Astrophysics Data System (ADS)

Khoury, Jed

2017-05-01

In this paper, we propose architectures for the implementation 16 Boolean optical gates from two inputs using externally pumped phase- conjugate Michelson interferometer. Depending on the gate to be implemented, some require single stage interferometer and others require two stages interferometer. The proposed optical gates can be used in several applications in optical networks including, but not limited to, all-optical packet routers switching, and all-optical error detection. The optical logic gates can also be used in recognition of noiseless rotation and scale invariant objects such as finger prints for home land security applications.

A Novel Implementation of Efficient Algorithms for Quantum Circuit Synthesis

NASA Astrophysics Data System (ADS)

Zeller, Luke

In this project, we design and develop a computer program to effectively approximate arbitrary quantum gates using the discrete set of Clifford Gates together with the T gate (π/8 gate). Employing recent results from Mosca et. al. and Giles and Selinger, we implement a decomposition scheme that outputs a sequence of Clifford, T, and Tt gates that approximate the input to within a specified error range ɛ. Specifically, the given gate is first rounded to an element of Z[1/2, i] with a precision determined by ɛ, and then exact synthesis is employed to produce the resulting gate. It is known that this procedure is optimal in approximating an arbitrary single qubit gate. Our program, written in Matlab and Python, can complete both approximate and exact synthesis of qubits. It can be used to assist in the experimental implementation of an arbitrary fault-tolerant single qubit gate, for which direct implementation isn't feasible.

On the inherent competition between valid and spurious inductive inferences in Boolean data

NASA Astrophysics Data System (ADS)

Andrecut, M.

Inductive inference is the process of extracting general rules from specific observations. This problem also arises in the analysis of biological networks, such as genetic regulatory networks, where the interactions are complex and the observations are incomplete. A typical task in these problems is to extract general interaction rules as combinations of Boolean covariates, that explain a measured response variable. The inductive inference process can be considered as an incompletely specified Boolean function synthesis problem. This incompleteness of the problem will also generate spurious inferences, which are a serious threat to valid inductive inference rules. Using random Boolean data as a null model, here we attempt to measure the competition between valid and spurious inductive inference rules from a given data set. We formulate two greedy search algorithms, which synthesize a given Boolean response variable in a sparse disjunct normal form, and respectively a sparse generalized algebraic normal form of the variables from the observation data, and we evaluate numerically their performance.

Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.

PubMed

Park, Inho; Lee, Kwang H; Lee, Doheon

2010-06-15

Gene set analysis has become an important tool for the functional interpretation of high-throughput gene expression datasets. Moreover, pattern analyses based on inferred gene set activities of individual samples have shown the ability to identify more robust disease signatures than individual gene-based pattern analyses. Although a number of approaches have been proposed for gene set-based pattern analysis, the combinatorial influence of deregulated gene sets on disease phenotype classification has not been studied sufficiently. We propose a new approach for inferring combinatorial Boolean rules of gene sets for a better understanding of cancer transcriptome and cancer classification. To reduce the search space of the possible Boolean rules, we identify small groups of gene sets that synergistically contribute to the classification of samples into their corresponding phenotypic groups (such as normal and cancer). We then measure the significance of the candidate Boolean rules derived from each group of gene sets; the level of significance is based on the class entropy of the samples selected in accordance with the rules. By applying the present approach to publicly available prostate cancer datasets, we identified 72 significant Boolean rules. Finally, we discuss several identified Boolean rules, such as the rule of glutathione metabolism (down) and prostaglandin synthesis regulation (down), which are consistent with known prostate cancer biology. Scripts written in Python and R are available at http://biosoft.kaist.ac.kr/~ihpark/. The refined gene sets and the full list of the identified Boolean rules are provided in the Supplementary Material. Supplementary data are available at Bioinformatics online.

A library of programmable DNAzymes that operate in a cellular environment.

PubMed

Kahan-Hanum, Maya; Douek, Yehonatan; Adar, Rivka; Shapiro, Ehud

2013-01-01

DNAzymes were used as inhibitory agents in a variety of experimental disease settings, such as cancer, viral infections and even HIV. Drugs that become active only upon the presence of preprogrammed abnormal environmental conditions may enable selective molecular therapy by targeting abnormal cells without injuring normal cells. Here we show a novel programmable DNAzyme library composed of variety of Boolean logic gates, including YES, AND, NOT, OR, NAND, ANDNOT, XOR, NOR and 3-input-AND gate, that uses both miRNAs and mRNAs as inputs. Each gate is based on the c-jun cleaving Dz13 DNAzyme and active only in the presence of specific input combinations. The library is modular, supports arbitrary inputs and outputs, cascadable, highly specific and robust. We demonstrate the library's potential diagnostic abilities on miRNA and mRNA combinations in cell lysate and its ability to operate in a cellular environment by using beacon-like c-jun mimicking substrate in living mammalian cells.

A library of programmable DNAzymes that operate in a cellular environment

PubMed Central

Kahan-Hanum, Maya; Douek, Yehonatan; Adar, Rivka; Shapiro, Ehud

2013-01-01

DNAzymes were used as inhibitory agents in a variety of experimental disease settings, such as cancer, viral infections and even HIV. Drugs that become active only upon the presence of preprogrammed abnormal environmental conditions may enable selective molecular therapy by targeting abnormal cells without injuring normal cells. Here we show a novel programmable DNAzyme library composed of variety of Boolean logic gates, including YES, AND, NOT, OR, NAND, ANDNOT, XOR, NOR and 3-input-AND gate, that uses both miRNAs and mRNAs as inputs. Each gate is based on the c-jun cleaving Dz13 DNAzyme and active only in the presence of specific input combinations. The library is modular, supports arbitrary inputs and outputs, cascadable, highly specific and robust. We demonstrate the library's potential diagnostic abilities on miRNA and mRNA combinations in cell lysate and its ability to operate in a cellular environment by using beacon-like c-jun mimicking substrate in living mammalian cells. PMID:23525068

Computing preimages of Boolean networks.

PubMed

Klotz, Johannes; Bossert, Martin; Schober, Steffen

2013-01-01

In this paper we present an algorithm based on the sum-product algorithm that finds elements in the preimage of a feed-forward Boolean networks given an output of the network. Our probabilistic method runs in linear time with respect to the number of nodes in the network. We evaluate our algorithm for randomly constructed Boolean networks and a regulatory network of Escherichia coli and found that it gives a valid solution in most cases.

Complete all-optical processing polarization-based binary logic gates and optical processors.

PubMed

Zaghloul, Y A; Zaghloul, A R M

2006-10-16

We present a complete all-optical-processing polarization-based binary-logic system, by which any logic gate or processor can be implemented. Following the new polarization-based logic presented in [Opt. Express 14, 7253 (2006)], we develop a new parallel processing technique that allows for the creation of all-optical-processing gates that produce a unique output either logic 1 or 0 only once in a truth table, and those that do not. This representation allows for the implementation of simple unforced OR, AND, XOR, XNOR, inverter, and more importantly NAND and NOR gates that can be used independently to represent any Boolean expression or function. In addition, the concept of a generalized gate is presented which opens the door for reconfigurable optical processors and programmable optical logic gates. Furthermore, the new design is completely compatible with the old one presented in [Opt. Express 14, 7253 (2006)], and with current semiconductor based devices. The gates can be cascaded, where the information is always on the laser beam. The polarization of the beam, and not its intensity, carries the information. The new methodology allows for the creation of multiple-input-multiple-output processors that implement, by itself, any Boolean function, such as specialized or non-specialized microprocessors. Three all-optical architectures are presented: orthoparallel optical logic architecture for all known and unknown binary gates, singlebranch architecture for only XOR and XNOR gates, and the railroad (RR) architecture for polarization optical processors (POP). All the control inputs are applied simultaneously leading to a single time lag which leads to a very-fast and glitch-immune POP. A simple and easy-to-follow step-by-step algorithm is provided for the POP, and design reduction methodologies are briefly discussed. The algorithm lends itself systematically to software programming and computer-assisted design. As examples, designs of all binary gates, multiple-input gates, and sequential and non-sequential Boolean expressions are presented and discussed. The operation of each design is simply understood by a bullet train traveling at the speed of light on a railroad system preconditioned by the crossover states predetermined by the control inputs. The presented designs allow for optical processing of the information eliminating the need to convert it, back and forth, to an electronic signal for processing purposes. All gates with a truth table, including for example Fredkin, Toffoli, testable reversible logic, and threshold logic gates, can be designed and implemented using the railroad architecture. That includes any future gates not known today. Those designs and the quantum gates are not discussed in this paper.

A Boolean Consistent Fuzzy Inference System for Diagnosing Diseases and Its Application for Determining Peritonitis Likelihood

PubMed Central

Dragović, Ivana; Turajlić, Nina; Pilčević, Dejan; Petrović, Bratislav; Radojević, Dragan

2015-01-01

Fuzzy inference systems (FIS) enable automated assessment and reasoning in a logically consistent manner akin to the way in which humans reason. However, since no conventional fuzzy set theory is in the Boolean frame, it is proposed that Boolean consistent fuzzy logic should be used in the evaluation of rules. The main distinction of this approach is that it requires the execution of a set of structural transformations before the actual values can be introduced, which can, in certain cases, lead to different results. While a Boolean consistent FIS could be used for establishing the diagnostic criteria for any given disease, in this paper it is applied for determining the likelihood of peritonitis, as the leading complication of peritoneal dialysis (PD). Given that patients could be located far away from healthcare institutions (as peritoneal dialysis is a form of home dialysis) the proposed Boolean consistent FIS would enable patients to easily estimate the likelihood of them having peritonitis (where a high likelihood would suggest that prompt treatment is indicated), when medical experts are not close at hand. PMID:27069500

Exploiting Surroundedness for Saliency Detection: A Boolean Map Approach.

PubMed

Zhang, Jianming; Sclaroff, Stan

2016-05-01

We demonstrate the usefulness of surroundedness for eye fixation prediction by proposing a Boolean Map based Saliency model (BMS). In our formulation, an image is characterized by a set of binary images, which are generated by randomly thresholding the image's feature maps in a whitened feature space. Based on a Gestalt principle of figure-ground segregation, BMS computes a saliency map by discovering surrounded regions via topological analysis of Boolean maps. Furthermore, we draw a connection between BMS and the Minimum Barrier Distance to provide insight into why and how BMS can properly captures the surroundedness cue via Boolean maps. The strength of BMS is verified by its simplicity, efficiency and superior performance compared with 10 state-of-the-art methods on seven eye tracking benchmark datasets.

Graphene-based room-temperature implementation of a modified Deutsch-Jozsa quantum algorithm.

PubMed

Dragoman, Daniela; Dragoman, Mircea

2015-12-04

We present an implementation of a one-qubit and two-qubit modified Deutsch-Jozsa quantum algorithm based on graphene ballistic devices working at room temperature. The modified Deutsch-Jozsa algorithm decides whether a function, equivalent to the effect of an energy potential distribution on the wave function of ballistic charge carriers, is constant or not, without measuring the output wave function. The function need not be Boolean. Simulations confirm that the algorithm works properly, opening the way toward quantum computing at room temperature based on the same clean-room technologies as those used for fabrication of very-large-scale integrated circuits.

Floating point only SIMD instruction set architecture including compare, select, Boolean, and alignment operations

DOEpatents

Gschwind, Michael K [Chappaqua, NY

2011-03-01

Mechanisms for implementing a floating point only single instruction multiple data instruction set architecture are provided. A processor is provided that comprises an issue unit, an execution unit coupled to the issue unit, and a vector register file coupled to the execution unit. The execution unit has logic that implements a floating point (FP) only single instruction multiple data (SIMD) instruction set architecture (ISA). The floating point vector registers of the vector register file store both scalar and floating point values as vectors having a plurality of vector elements. The processor may be part of a data processing system.

Demonstration of Inexact Computing Implemented in the JPEG Compression Algorithm using Probabilistic Boolean Logic applied to CMOS Components

DTIC Science & Technology

2015-12-24

Signal to Noise Ratio SPICE Simulation Program with Integrated Circuit Emphasis TIFF Tagged Image File Format USC University of Southern California xvii...sources can create errors in digital circuits. These effects can be simulated using Simulation Program with Integrated Circuit Emphasis ( SPICE ) or...compute summary statistics. 4.1 Circuit Simulations Noisy analog circuits can be simulated in SPICE or Cadence SpectreTM software via noisy voltage

PSPVDC: An Adaptation of the PSP that Incorporates Verified Design by Contract

DTIC Science & Technology

2013-05-01

characteristics mentioned above, including the following: • Java Modeling Language (JML) implements DbC in Java . VDbC can then be carried out using tools like...Extended Static Checking (ESC/ Java ) [Cok 2005] or TACO [Galeotti 2010]. • Perfect Developer [Crocker 2003] is a specification and modeling language...These are written in the language employed in the environment (e.g., as Java Boolean expressions, if JML is used) which we call the carrier lan

"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

PubMed Central

2011-01-01

Background In Thomas' formalism for modeling gene regulatory networks (GRNs), branching time, where a state can have more than one possible future, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such as (a) asynchrony, (b) incompletely specified behavior, and (c) interaction with the environment. Introducing more than one possible future for a state, however, creates a difficulty for ordinary simulators, because infinitely many paths may appear, limiting ordinary simulators to statistical conclusions. Model checkers for branching time, by contrast, are able to prove properties in the presence of infinitely many paths. Results We have developed Antelope ("Analysis of Networks through TEmporal-LOgic sPEcifications", http://turing.iimas.unam.mx:8080/AntelopeWEB/), a model checker for analyzing and constructing Boolean GRNs. Currently, software systems for Boolean GRNs use branching time almost exclusively for asynchrony. Antelope, by contrast, also uses branching time for incompletely specified behavior and environment interaction. We show the usefulness of modeling these two phenomena in the development of a Boolean GRN of the Arabidopsis thaliana root stem cell niche. There are two obstacles to a direct approach when applying model checking to Boolean GRN analysis. First, ordinary model checkers normally only verify whether or not a given set of model states has a given property. In comparison, a model checker for Boolean GRNs is preferable if it reports the set of states having a desired property. Second, for efficiency, the expressiveness of many model checkers is limited, resulting in the inability to express some interesting properties of Boolean GRNs. Antelope tries to overcome these two drawbacks: Apart from reporting the set of all states having a given property, our model checker can express, at the expense of efficiency, some properties that ordinary model checkers (e.g., NuSMV) cannot. This additional expressiveness is achieved by employing a logic extending the standard Computation-Tree Logic (CTL) with hybrid-logic operators. Conclusions We illustrate the advantages of Antelope when (a) modeling incomplete networks and environment interaction, (b) exhibiting the set of all states having a given property, and (c) representing Boolean GRN properties with hybrid CTL. PMID:22192526

Jimena: efficient computing and system state identification for genetic regulatory networks.

PubMed

Karl, Stefan; Dandekar, Thomas

2013-10-11

Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.

Experiments with arbitrary networks in time-multiplexed delay systems

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Schmadel, Don C.; Murphy, Thomas E.; Roy, Rajarshi

2017-12-01

We report a new experimental approach using an optoelectronic feedback loop to investigate the dynamics of oscillators coupled on large complex networks with arbitrary topology. Our implementation is based on a single optoelectronic feedback loop with time delays. We use the space-time interpretation of systems with time delay to create large networks of coupled maps. Others have performed similar experiments using high-pass filters to implement the coupling; this restricts the network topology to the coupling of only a few nearest neighbors. In our experiment, the time delays and coupling are implemented on a field-programmable gate array, allowing the creation of networks with arbitrary coupling topology. This system has many advantages: the network nodes are truly identical, the network is easily reconfigurable, and the network dynamics occur at high speeds. We use this system to study cluster synchronization and chimera states in both small and large networks of different topologies.

Theory and calculus of cubical complexes

NASA Technical Reports Server (NTRS)

Perlman, M.

1973-01-01

Combination switching networks with multiple outputs may be represented by Boolean functions. Report has been prepared which describes derivation and use of extraction algorithm that may be adapted to simplification of such simultaneous Boolean functions.

Dynamic Boolean Mathematics

ERIC Educational Resources Information Center

Bossé, Michael J.; Adu-Gyamfi, Kwaku; Chandler, Kayla; Lynch-Davis, Kathleen

2016-01-01

Dynamic mathematical environments allow users to reify mathematical concepts through multiple representations, transform mathematical relations and organically explore mathematical properties, investigate integrated mathematics, and develop conceptual understanding. Herein, we integrate Boolean algebra, the functionalities of a dynamic…

Total Parenteral Nutrition

MedlinePlus

... Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy) at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess ...

Complexity and approximability of quantified and stochastic constraint satisfaction problems

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

Hunt, H. B.; Stearns, R. L.; Marathe, M. V.

2001-01-01

Let D be an arbitrary (not necessarily finite) nonempty set, let C be a finite set of constant symbols denoting arbitrary elements of D, and let S be an arbitrary finite set of finite-arity relations on D. We denote the problem of determining the satisfiability of finite conjunctions of relations in S applied to variables (to variables and symbols in C) by SAT(S) (by SAT{sub c}(S)). Here, we study simultaneously the complexity of and the existence of efficient approximation algorithms for a number of variants of the problems SAT(S) and SAT{sub c}(S), and for many different D, C, and S.more » These problem variants include decision and optimization problems, for formulas, quantified formulas stochastically-quantified formulas. We denote these problems by Q-SAT(S), MAX-Q-SAT(S), S-SAT(S), MAX-S-SAT(S) MAX-NSF-Q-SAT(S) and MAX-NSF-S-SAT(S). The main contribution is the development of a unified predictive theory for characterizing the the complexity of these problems. Our unified approach is based on the following basic two basic concepts: (i) strongly-local replacements/reductions and (ii) relational/algebraic representability. Let k {ge} 2. Let S be a finite set of finite-arity relations on {Sigma}{sub k} with the following condition on S: All finite arity relations on {Sigma}{sub k} can be represented as finite existentially-quantified conjunctions of relations in S applied to variables (to variables and constant symbols in C), Then we prove the following new results: (1) The problems SAT(S) and SAT{sub c}(S) are both NQL-complete and {le}{sub logn}{sup bw}-complete for NP. (2) The problems Q-SAT(S), Q-SAT{sub c}(S), are PSPACE-complete. Letting k = 2, the problem S-SAT(S) and S-SAT{sub c}(S) are PSPACE-complete. (3) {exists} {epsilon} > 0 for which approximating the problems MAX-Q-SAT(S) within {epsilon} times optimum is PSPACE-hard. Letting k =: 2, {exists} {epsilon} > 0 for which approximating the problems MAX-S-SAT(S) within {epsilon} times optimum is PSPACE-hard. (4) {forall} {epsilon} > 0 the problems MAX-NSF-Q-SAT(S) and MAX-NSF-S-SAT(S), are PSPACE-hard to approximate within a factor of n{sup {epsilon}} times optimum. These results significantly extend the earlier results by (i) Papadimitriou [Pa851] on complexity of stochastic satisfiability, (ii) Condon, Feigenbaum, Lund and Shor [CF+93, CF+94] by identifying natural classes of PSPACE-hard optimization problems with provably PSPACE-hard {epsilon}-approximation problems. Moreover, most of our results hold not just for Boolean relations: most previous results were done only in the context of Boolean domains. The results also constitute as a significant step towards obtaining a dichotomy theorems for the problems MAX-S-SAT(S) and MAX-Q-SAT(S): a research area of recent interest [CF+93, CF+94, Cr95, KSW97, LMP99].« less

General method to find the attractors of discrete dynamic models of biological systems.

PubMed

Gan, Xiao; Albert, Réka

2018-04-01

Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

General method to find the attractors of discrete dynamic models of biological systems

NASA Astrophysics Data System (ADS)

Gan, Xiao; Albert, Réka

2018-04-01

Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.

PubMed

Müssel, Christoph; Hopfensitz, Martin; Kestler, Hans A

2010-05-15

As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide deep insights into the functioning of cells. The dynamics of gene expression, for example, can be modeled with Boolean networks (BNs). These are mathematical models of low complexity, but have the advantage of being able to capture essential properties of gene-regulatory networks. However, current implementations of BNs only focus on different sub-aspects of this model and do not allow for a seamless integration into existing preprocessing pipelines. BoolNet efficiently integrates methods for synchronous, asynchronous and probabilistic BNs. This includes reconstructing networks from time series, generating random networks, robustness analysis via perturbation, Markov chain simulations, and identification and visualization of attractors. The package BoolNet is freely available from the R project at http://cran.r-project.org/ or http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/ under Artistic License 2.0. hans.kestler@uni-ulm.de Supplementary data are available at Bioinformatics online.

A genetic code Boolean structure. II. The genetic information system as a Boolean information system.

PubMed

Sanchez, Robersy; Grau, Ricardo

2005-09-01

A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96 x 10(25) bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy Ei (i=1,2,...,20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy Ei so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

Ordinary differential equations and Boolean networks in application to modelling of 6-mercaptopurine metabolism.

PubMed

Lavrova, Anastasia I; Postnikov, Eugene B; Zyubin, Andrey Yu; Babak, Svetlana V

2017-04-01

We consider two approaches to modelling the cell metabolism of 6-mercaptopurine, one of the important chemotherapy drugs used for treating acute lymphocytic leukaemia: kinetic ordinary differential equations, and Boolean networks supplied with one controlling node, which takes continual values. We analyse their interplay with respect to taking into account ATP concentration as a key parameter of switching between different pathways. It is shown that the Boolean networks, which allow avoiding the complexity of general kinetic modelling, preserve the possibility of reproducing the principal switching mechanism.

Improving the quantum cost of reversible Boolean functions using reorder algorithm

NASA Astrophysics Data System (ADS)

Ahmed, Taghreed; Younes, Ahmed; Elsayed, Ashraf

2018-05-01

This paper introduces a novel algorithm to synthesize a low-cost reversible circuits for any Boolean function with n inputs represented as a Positive Polarity Reed-Muller expansion. The proposed algorithm applies a predefined rules to reorder the terms in the function to minimize the multi-calculation of common parts of the Boolean function to decrease the quantum cost of the reversible circuit. The paper achieves a decrease in the quantum cost and/or the circuit length, on average, when compared with relevant work in the literature.

Volumetric T-spline Construction Using Boolean Operations

DTIC Science & Technology

2013-07-01

SUBTITLE Volumetric T-spline Construction Using Boolean Operations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...Acknowledgements The work of L. Liu and Y. Zhang was supported by ONR-YIP award N00014- 10-1-0698 and an ONR Grant N00014-08-1-0653. T. J.R. Hughes was sup- 16...T-spline Construction Using Boolean Operations 17 ported by ONR Grant N00014-08-1-0992, NSF GOALI CMI-0700807/0700204, NSF CMMI-1101007 and a SINTEF

Cascaded all-optical operations in a hybrid integrated 80-Gb/s logic circuit.

PubMed

LeGrange, J D; Dinu, M; Sochor, T; Bollond, P; Kasper, A; Cabot, S; Johnson, G S; Kang, I; Grant, A; Kay, J; Jaques, J

2014-06-02

We demonstrate logic functionalities in a high-speed all-optical logic circuit based on differential Mach-Zehnder interferometers with semiconductor optical amplifiers as the nonlinear optical elements. The circuit, implemented by hybrid integration of the semiconductor optical amplifiers on a planar lightwave circuit platform fabricated in silica glass, can be flexibly configured to realize a variety of Boolean logic gates. We present both simulations and experimental demonstrations of cascaded all-optical operations for 80-Gb/s on-off keyed data.

Realisation of all 16 Boolean logic functions in a single magnetoresistance memory cell

NASA Astrophysics Data System (ADS)

Gao, Shuang; Yang, Guang; Cui, Bin; Wang, Shouguo; Zeng, Fei; Song, Cheng; Pan, Feng

2016-06-01

Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future.Stateful logic circuits based on next-generation nonvolatile memories, such as magnetoresistance random access memory (MRAM), promise to break the long-standing von Neumann bottleneck in state-of-the-art data processing devices. For the successful commercialisation of stateful logic circuits, a critical step is realizing the best use of a single memory cell to perform logic functions. In this work, we propose a method for implementing all 16 Boolean logic functions in a single MRAM cell, namely a magnetoresistance (MR) unit. Based on our experimental results, we conclude that this method is applicable to any MR unit with a double-hump-like hysteresis loop, especially pseudo-spin-valve magnetic tunnel junctions with a high MR ratio. Moreover, after simply reversing the correspondence between voltage signals and output logic values, this method could also be applicable to any MR unit with a double-pit-like hysteresis loop. These results may provide a helpful solution for the final commercialisation of MRAM-based stateful logic circuits in the near future. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03169b

Dynamic Network-Based Epistasis Analysis: Boolean Examples

PubMed Central

Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

2011-01-01

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and single-path assumption, but also by demonstrating the importance of considering temporal dynamics, and specifically introducing the usefulness of Boolean network models and also reviewing some key properties of network approaches. PMID:22645556

Acoustic logic gates and Boolean operation based on self-collimating acoustic beams

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

Zhang, Ting; Xu, Jian-yi; Cheng, Ying, E-mail: chengying@nju.edu.cn

2015-03-16

The reveal of self-collimation effect in two-dimensional (2D) photonic or acoustic crystals has opened up possibilities for signal manipulation. In this paper, we have proposed acoustic logic gates based on the linear interference of self-collimated beams in 2D sonic crystals (SCs) with line-defects. The line defects on the diagonal of the 2D square SCs are actually functioning as a 3 dB splitter. By adjusting the phase difference between two input signals, the basic Boolean logic functions such as XOR, OR, AND, and NOT are achieved both theoretically and experimentally. Due to the non-diffracting property of self-collimation beams, more complex Boolean logicmore » and algorithms such as NAND, NOR, and XNOR can be realized by cascading the basic logic gates. The achievement of acoustic logic gates and Boolean operation provides a promising approach for acoustic signal computing and manipulations.« less

Boolean networks with veto functions

NASA Astrophysics Data System (ADS)

Ebadi, Haleh; Klemm, Konstantin

2014-08-01

Boolean networks are discrete dynamical systems for modeling regulation and signaling in living cells. We investigate a particular class of Boolean functions with inhibiting inputs exerting a veto (forced zero) on the output. We give analytical expressions for the sensitivity of these functions and provide evidence for their role in natural systems. In an intracellular signal transduction network [Helikar et al., Proc. Natl. Acad. Sci. USA 105, 1913 (2008), 10.1073/pnas.0705088105], the functions with veto are over-represented by a factor exceeding the over-representation of threshold functions and canalyzing functions in the same system. In Boolean networks for control of the yeast cell cycle [Li et al., Proc. Natl. Acad. Sci. USA 101, 4781 (2004), 10.1073/pnas.0305937101; Davidich et al., PLoS ONE 3, e1672 (2008), 10.1371/journal.pone.0001672], no or minimal changes to the wiring diagrams are necessary to formulate their dynamics in terms of the veto functions introduced here.

Data-Driven Sampling Matrix Boolean Optimization for Energy-Efficient Biomedical Signal Acquisition by Compressive Sensing.

PubMed

Wang, Yuhao; Li, Xin; Xu, Kai; Ren, Fengbo; Yu, Hao

2017-04-01

Compressive sensing is widely used in biomedical applications, and the sampling matrix plays a critical role on both quality and power consumption of signal acquisition. It projects a high-dimensional vector of data into a low-dimensional subspace by matrix-vector multiplication. An optimal sampling matrix can ensure accurate data reconstruction and/or high compression ratio. Most existing optimization methods can only produce real-valued embedding matrices that result in large energy consumption during data acquisition. In this paper, we propose an efficient method that finds an optimal Boolean sampling matrix in order to reduce the energy consumption. Compared to random Boolean embedding, our data-driven Boolean sampling matrix can improve the image recovery quality by 9 dB. Moreover, in terms of sampling hardware complexity, it reduces the energy consumption by 4.6× and the silicon area by 1.9× over the data-driven real-valued embedding.

Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors.

PubMed

Sun, Mengyang; Cheng, Xianrui; Socolar, Joshua E S

2013-06-01

A common approach to the modeling of gene regulatory networks is to represent activating or repressing interactions using ordinary differential equations for target gene concentrations that include Hill function dependences on regulator gene concentrations. An alternative formulation represents the same interactions using Boolean logic with time delays associated with each network link. We consider the attractors that emerge from the two types of models in the case of a simple but nontrivial network: a figure-8 network with one positive and one negative feedback loop. We show that the different modeling approaches give rise to the same qualitative set of attractors with the exception of a possible fixed point in the ordinary differential equation model in which concentrations sit at intermediate values. The properties of the attractors are most easily understood from the Boolean perspective, suggesting that time-delay Boolean modeling is a useful tool for understanding the logic of regulatory networks.

An efficient algorithm for computing fixed length attractors based on bounded model checking in synchronous Boolean networks with biochemical applications.

PubMed

Li, X Y; Yang, G W; Zheng, D S; Guo, W S; Hung, W N N

2015-04-28

Genetic regulatory networks are the key to understanding biochemical systems. One condition of the genetic regulatory network under different living environments can be modeled as a synchronous Boolean network. The attractors of these Boolean networks will help biologists to identify determinant and stable factors. Existing methods identify attractors based on a random initial state or the entire state simultaneously. They cannot identify the fixed length attractors directly. The complexity of including time increases exponentially with respect to the attractor number and length of attractors. This study used the bounded model checking to quickly locate fixed length attractors. Based on the SAT solver, we propose a new algorithm for efficiently computing the fixed length attractors, which is more suitable for large Boolean networks and numerous attractors' networks. After comparison using the tool BooleNet, empirical experiments involving biochemical systems demonstrated the feasibility and efficiency of our approach.

The exact fundamental solution for the Benes tracking problem

NASA Astrophysics Data System (ADS)

Balaji, Bhashyam

2009-05-01

The universal continuous-discrete tracking problem requires the solution of a Fokker-Planck-Kolmogorov forward equation (FPKfe) for an arbitrary initial condition. Using results from quantum mechanics, the exact fundamental solution for the FPKfe is derived for the state model of arbitrary dimension with Benes drift that requires only the computation of elementary transcendental functions and standard linear algebra techniques- no ordinary or partial differential equations need to be solved. The measurement process may be an arbitrary, discrete-time nonlinear stochastic process, and the time step size can be arbitrary. Numerical examples are included, demonstrating its utility in practical implementation.

High-Density Liquid-State Machine Circuitry for Time-Series Forecasting.

PubMed

Rosselló, Josep L; Alomar, Miquel L; Morro, Antoni; Oliver, Antoni; Canals, Vincent

2016-08-01

Spiking neural networks (SNN) are the last neural network generation that try to mimic the real behavior of biological neurons. Although most research in this area is done through software applications, it is in hardware implementations in which the intrinsic parallelism of these computing systems are more efficiently exploited. Liquid state machines (LSM) have arisen as a strategic technique to implement recurrent designs of SNN with a simple learning methodology. In this work, we show a new low-cost methodology to implement high-density LSM by using Boolean gates. The proposed method is based on the use of probabilistic computing concepts to reduce hardware requirements, thus considerably increasing the neuron count per chip. The result is a highly functional system that is applied to high-speed time series forecasting.

A transition calculus for Boolean functions. [logic circuit analysis

NASA Technical Reports Server (NTRS)

Tucker, J. H.; Bennett, A. W.

1974-01-01

A transition calculus is presented for analyzing the effect of input changes on the output of logic circuits. The method is closely related to the Boolean difference, but it is more powerful. Both differentiation and integration are considered.

Inferring Boolean network states from partial information

PubMed Central

2013-01-01

Networks of molecular interactions regulate key processes in living cells. Therefore, understanding their functionality is a high priority in advancing biological knowledge. Boolean networks are often used to describe cellular networks mathematically and are fitted to experimental datasets. The fitting often results in ambiguities since the interpretation of the measurements is not straightforward and since the data contain noise. In order to facilitate a more reliable mapping between datasets and Boolean networks, we develop an algorithm that infers network trajectories from a dataset distorted by noise. We analyze our algorithm theoretically and demonstrate its accuracy using simulation and microarray expression data. PMID:24006954

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

PubMed Central

Mushthofa, Mushthofa; Torres, Gustavo; Van de Peer, Yves; Marchal, Kathleen; De Cock, Martine

2014-01-01

Motivation: Boolean network models are suitable to simulate GRNs in the absence of detailed kinetic information. However, reducing the biological reality implies making assumptions on how genes interact (interaction rules) and how their state is updated during the simulation (update scheme). The exact choice of the assumptions largely determines the outcome of the simulations. In most cases, however, the biologically correct assumptions are unknown. An ideal simulation thus implies testing different rules and schemes to determine those that best capture an observed biological phenomenon. This is not trivial because most current methods to simulate Boolean network models of GRNs and to compute their attractors impose specific assumptions that cannot be easily altered, as they are built into the system. Results: To allow for a more flexible simulation framework, we developed ASP-G. We show the correctness of ASP-G in simulating Boolean network models and obtaining attractors under different assumptions by successfully recapitulating the detection of attractors of previously published studies. We also provide an example of how performing simulation of network models under different settings help determine the assumptions under which a certain conclusion holds. The main added value of ASP-G is in its modularity and declarativity, making it more flexible and less error-prone than traditional approaches. The declarative nature of ASP-G comes at the expense of being slower than the more dedicated systems but still achieves a good efficiency with respect to computational time. Availability and implementation: The source code of ASP-G is available at http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip. Contact: Kathleen.Marchal@UGent.be or Martine.DeCock@UGent.be Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25028722

Quantum algorithms on Walsh transform and Hamming distance for Boolean functions

NASA Astrophysics Data System (ADS)

Xie, Zhengwei; Qiu, Daowen; Cai, Guangya

2018-06-01

Walsh spectrum or Walsh transform is an alternative description of Boolean functions. In this paper, we explore quantum algorithms to approximate the absolute value of Walsh transform W_f at a single point z0 (i.e., |W_f(z0)|) for n-variable Boolean functions with probability at least 8/π 2 using the number of O(1/|W_f(z_{0)|ɛ }) queries, promised that the accuracy is ɛ , while the best known classical algorithm requires O(2n) queries. The Hamming distance between Boolean functions is used to study the linearity testing and other important problems. We take advantage of Walsh transform to calculate the Hamming distance between two n-variable Boolean functions f and g using O(1) queries in some cases. Then, we exploit another quantum algorithm which converts computing Hamming distance between two Boolean functions to quantum amplitude estimation (i.e., approximate counting). If Ham(f,g)=t≠0, we can approximately compute Ham( f, g) with probability at least 2/3 by combining our algorithm and {Approx-Count(f,ɛ ) algorithm} using the expected number of Θ( √{N/(\\lfloor ɛ t\\rfloor +1)}+√{t(N-t)}/\\lfloor ɛ t\\rfloor +1) queries, promised that the accuracy is ɛ . Moreover, our algorithm is optimal, while the exact query complexity for the above problem is Θ(N) and the query complexity with the accuracy ɛ is O(1/ɛ 2N/(t+1)) in classical algorithm, where N=2n. Finally, we present three exact quantum query algorithms for two promise problems on Hamming distance using O(1) queries, while any classical deterministic algorithm solving the problem uses Ω(2n) queries.

Development of Boolean calculus and its applications. [digital systems design

NASA Technical Reports Server (NTRS)

Tapia, M. A.

1980-01-01

The development of Boolean calculus for its application to developing digital system design methodologies that would reduce system complexity, size, cost, speed, power requirements, etc., is discussed. Synthesis procedures for logic circuits are examined particularly asynchronous circuits using clock triggered flip flops.

Advanced Feedback Methods in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1985-01-01

In this study, automatic feedback techniques are applied to Boolean query statements in online information retrieval to generate improved query statements based on information contained in previously retrieved documents. Feedback operations are carried out using conventional Boolean logic and extended logic. Experimental output is included to…

Phase transition in NK-Kauffman networks and its correction for Boolean irreducibility

NASA Astrophysics Data System (ADS)

Zertuche, Federico

2014-05-01

In a series of articles published in 1986, Derrida and his colleagues studied two mean field treatments (the quenched and the annealed) for NK-Kauffman networks. Their main results lead to a phase transition curve Kc 2 pc(1-pc)=1 (0

Controllability and observability of Boolean networks arising from biology

NASA Astrophysics Data System (ADS)

Li, Rui; Yang, Meng; Chu, Tianguang

2015-02-01

Boolean networks are currently receiving considerable attention as a computational scheme for system level analysis and modeling of biological systems. Studying control-related problems in Boolean networks may reveal new insights into the intrinsic control in complex biological systems and enable us to develop strategies for manipulating biological systems using exogenous inputs. This paper considers controllability and observability of Boolean biological networks. We propose a new approach, which draws from the rich theory of symbolic computation, to solve the problems. Consequently, simple necessary and sufficient conditions for reachability, controllability, and observability are obtained, and algorithmic tests for controllability and observability which are based on the Gröbner basis method are presented. As practical applications, we apply the proposed approach to several different biological systems, namely, the mammalian cell-cycle network, the T-cell activation network, the large granular lymphocyte survival signaling network, and the Drosophila segment polarity network, gaining novel insights into the control and/or monitoring of the specific biological systems.

Solving a discrete model of the lac operon using Z3

NASA Astrophysics Data System (ADS)

Gutierrez, Natalia A.

2014-05-01

A discrete model for the Lcac Operon is solved using the SMT-solver Z3. Traditionally the Lac Operon is formulated in a continuous math model. This model is a system of ordinary differential equations. Here, it was considerated as a discrete model, based on a Boolean red. The biological problem of Lac Operon is enunciated as a problem of Boolean satisfiability, and it is solved using an STM-solver named Z3. Z3 is a powerful solver that allows understanding the basic dynamic of the Lac Operon in an easier and more efficient way. The multi-stability of the Lac Operon can be easily computed with Z3. The code that solves the Boolean red can be written in Python language or SMT-Lib language. Both languages were used in local version of the program as online version of Z3. For future investigations it is proposed to solve the Boolean red of Lac Operon using others SMT-solvers as cvc4, alt-ergo, mathsat and yices.

Perturbation propagation in random and evolved Boolean networks

NASA Astrophysics Data System (ADS)

Fretter, Christoph; Szejka, Agnes; Drossel, Barbara

2009-03-01

In this paper, we investigate the propagation of perturbations in Boolean networks by evaluating the Derrida plot and its modifications. We show that even small random Boolean networks agree well with the predictions of the annealed approximation, but nonrandom networks show a very different behaviour. We focus on networks that were evolved for high dynamical robustness. The most important conclusion is that the simple distinction between frozen, critical and chaotic networks is no longer useful, since such evolved networks can display the properties of all three types of networks. Furthermore, we evaluate a simplified empirical network and show how its specific state space properties are reflected in the modified Derrida plots.

Implementing a Loosely Coupled Fluid Structure Interaction Finite Element Model in PHASTA

NASA Astrophysics Data System (ADS)

Pope, David

Fluid Structure Interaction problems are an important multi-physics phenomenon in the design of aerospace vehicles and other engineering applications. A variety of computational fluid dynamics solvers capable of resolving the fluid dynamics exist. PHASTA is one such computational fluid dynamics solver. Enhancing the capability of PHASTA to resolve Fluid-Structure Interaction first requires implementing a structural dynamics solver. The implementation also requires a correction of the mesh used to solve the fluid equations to account for the deformation of the structure. This results in mesh motion and causes the need for an Arbitrary Lagrangian-Eulerian modification to the fluid dynamics equations currently implemented in PHASTA. With the implementation of both structural dynamics physics, mesh correction, and the Arbitrary Lagrangian-Eulerian modification of the fluid dynamics equations, PHASTA is made capable of solving Fluid-Structure Interaction problems.

Toxicological Tipping Points: Learning Boolean Networks from High-Content Imaging Data. (BOSC meeting)

EPA Science Inventory

The objective of this work is to elucidate biological networks underlying cellular tipping points using time-course data. We discretized the high-content imaging (HCI) data and inferred Boolean networks (BNs) that could accurately predict dynamic cellular trajectories. We found t...

Boolean linear differential operators on elementary cellular automata

NASA Astrophysics Data System (ADS)

Martín Del Rey, Ángel

2014-12-01

In this paper, the notion of boolean linear differential operator (BLDO) on elementary cellular automata (ECA) is introduced and some of their more important properties are studied. Special attention is paid to those differential operators whose coefficients are the ECA with rule numbers 90 and 150.

Implementation of perfectly matched layers in an arbitrary geometrical boundary for elastic wave modelling

NASA Astrophysics Data System (ADS)

Gao, Hongwei; Zhang, Jianfeng

2008-09-01

The perfectly matched layer (PML) absorbing boundary condition is incorporated into an irregular-grid elastic-wave modelling scheme, thus resulting in an irregular-grid PML method. We develop the irregular-grid PML method using the local coordinate system based PML splitting equations and integral formulation of the PML equations. The irregular-grid PML method is implemented under a discretization of triangular grid cells, which has the ability to absorb incident waves in arbitrary directions. This allows the PML absorbing layer to be imposed along arbitrary geometrical boundaries. As a result, the computational domain can be constructed with smaller nodes, for instance, to represent the 2-D half-space by a semi-circle rather than a rectangle. By using a smooth artificial boundary, the irregular-grid PML method can also avoid the special treatments to the corners, which lead to complex computer implementations in the conventional PML method. We implement the irregular-grid PML method in both 2-D elastic isotropic and anisotropic media. The numerical simulations of a VTI lamb's problem, wave propagation in an isotropic elastic medium with curved surface and in a TTI medium demonstrate the good behaviour of the irregular-grid PML method.

Demonstration of Inexact Computing Implemented in the JPEG Compression Algorithm using Probabilistic Boolean Logic applied to CMOS Components

DTIC Science & Technology

2015-12-24

Ripple-Carry RCA Ripple-Carry Adder RF Radio Frequency RMS Root-Mean-Square SEU Single Event Upset SIPI Signal and Image Processing Institute SNR...correctness, where 0.5 < p < 1, and a probability (1−p) of error. Errors could be caused by noise, radio frequency (RF) interference, crosstalk...utilized in the Apollo Guidance Computer is the three input NOR Gate. . . At the time that the decision was made to use in- 11 tegrated circuits, the

Demonstration of Inexact Computing Implemented in the JPEG Compression Algorithm Using Probabilistic Boolean Logic Applied to CMOS Components

DTIC Science & Technology

2015-12-24

Ripple-Carry RCA Ripple-Carry Adder RF Radio Frequency RMS Root-Mean-Square SEU Single Event Upset SIPI Signal and Image Processing Institute SNR...correctness, where 0.5 < p < 1, and a probability (1−p) of error. Errors could be caused by noise, radio frequency (RF) interference, crosstalk...utilized in the Apollo Guidance Computer is the three input NOR Gate. . . At the time that the decision was made to use in- 11 tegrated circuits, the

Robust optimization with transiently chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Sumi, R.; Molnár, B.; Ercsey-Ravasz, M.

2014-05-01

Efficiently solving hard optimization problems has been a strong motivation for progress in analog computing. In a recent study we presented a continuous-time dynamical system for solving the NP-complete Boolean satisfiability (SAT) problem, with a one-to-one correspondence between its stable attractors and the SAT solutions. While physical implementations could offer great efficiency, the transiently chaotic dynamics raises the question of operability in the presence of noise, unavoidable on analog devices. Here we show that the probability of finding solutions is robust to noise intensities well above those present on real hardware. We also developed a cellular neural network model realizable with analog circuits, which tolerates even larger noise intensities. These methods represent an opportunity for robust and efficient physical implementations.

A C++11 implementation of arbitrary-rank tensors for high-performance computing

NASA Astrophysics Data System (ADS)

Aragón, Alejandro M.

2014-06-01

This article discusses an efficient implementation of tensors of arbitrary rank by using some of the idioms introduced by the recently published C++ ISO Standard (C++11). With the aims at providing a basic building block for high-performance computing, a single Array class template is carefully crafted, from which vectors, matrices, and even higher-order tensors can be created. An expression template facility is also built around the array class template to provide convenient mathematical syntax. As a result, by using templates, an extra high-level layer is added to the C++ language when dealing with algebraic objects and their operations, without compromising performance. The implementation is tested running on both CPU and GPU.

A C++11 implementation of arbitrary-rank tensors for high-performance computing

NASA Astrophysics Data System (ADS)

Aragón, Alejandro M.

2014-11-01

This article discusses an efficient implementation of tensors of arbitrary rank by using some of the idioms introduced by the recently published C++ ISO Standard (C++11). With the aims at providing a basic building block for high-performance computing, a single Array class template is carefully crafted, from which vectors, matrices, and even higher-order tensors can be created. An expression template facility is also built around the array class template to provide convenient mathematical syntax. As a result, by using templates, an extra high-level layer is added to the C++ language when dealing with algebraic objects and their operations, without compromising performance. The implementation is tested running on both CPU and GPU.

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…

Evolution of canalizing Boolean networks

NASA Astrophysics Data System (ADS)

Szejka, A.; Drossel, B.

2007-04-01

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive walk, which allows us to explore the fitness landscape. Mutations change the connections and the functions of the nodes. Our fitness criterion is the robustness of the dynamical attractors against small perturbations. We find that with this fitness criterion the global maximum is always reached and that there is a huge neutral space of 100% fitness. Furthermore, in spite of having such a high degree of robustness, the evolved networks still share many features with “chaotic” networks.

Circulant Matrices and Affine Equivalence of Monomial Rotation Symmetric Boolean Functions

DTIC Science & Technology

2015-01-01

definitions , including monomial rotation symmetric (MRS) Boolean functions and affine equivalence, and a known result for such quadratic functions...degree of the MRS is, we have a similar result as [40, Theorem 1.1] for n = 4p (p prime), or squarefree integers n, which along with our Theorem 5.2

User Practices in Keyword and Boolean Searching on an Online Public Access Catalog.

ERIC Educational Resources Information Center

Ensor, Pat

1992-01-01

Discussion of keyword and Boolean searching techniques in online public access catalogs (OPACs) focuses on a study conducted at Indiana State University that examined users' attitudes toward searching on NOTIS (Northwestern Online Total Integrated System). Relevant literature is reviewed, and implications for library instruction are suggested. (17…

Using Vector and Extended Boolean Matching in an Expert System for Selecting Foster Homes.

ERIC Educational Resources Information Center

Fox, Edward A.; Winett, Sheila G.

1990-01-01

Describes FOCES (Foster Care Expert System), a prototype expert system for choosing foster care placements for children which integrates information retrieval techniques with artificial intelligence. The use of prototypes and queries in Prolog routines, extended Boolean matching, and vector correlation are explained, as well as evaluation by…

A Construction of Boolean Functions with Good Cryptographic Properties

DTIC Science & Technology

2014-01-01

be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT...2008, LNCS 5350, Springer–Verlag, 2008, pp. 425–440. [10] C. Carlet and K. Feng, “An Infinite Class of Balanced Vectorial Boolean Functions with Optimum

Using computer algebra and SMT solvers in algebraic biology

NASA Astrophysics Data System (ADS)

Pineda Osorio, Mateo

2014-05-01

Biologic processes are represented as Boolean networks, in a discrete time. The dynamics within these networks are approached with the help of SMT Solvers and the use of computer algebra. Software such as Maple and Z3 was used in this case. The number of stationary states for each network was calculated. The network studied here corresponds to the immune system under the effects of drastic mood changes. Mood is considered as a Boolean variable that affects the entire dynamics of the immune system, changing the Boolean satisfiability and the number of stationary states of the immune network. Results obtained show Z3's great potential as a SMT Solver. Some of these results were verified in Maple, even though it showed not to be as suitable for the problem approach. The solving code was constructed using Z3-Python and Z3-SMT-LiB. Results obtained are important in biology systems and are expected to help in the design of immune therapies. As a future line of research, more complex Boolean network representations of the immune system as well as the whole psychological apparatus are suggested.

Therapeutic target discovery using Boolean network attractors: improvements of kali

PubMed Central

Guziolowski, Carito

2018-01-01

In a previous article, an algorithm for identifying therapeutic targets in Boolean networks modelling pathological mechanisms was introduced. In the present article, the improvements made on this algorithm, named kali, are described. These improvements are (i) the possibility to work on asynchronous Boolean networks, (ii) a finer assessment of therapeutic targets and (iii) the possibility to use multivalued logic. kali assumes that the attractors of a dynamical system, such as a Boolean network, are associated with the phenotypes of the modelled biological system. Given a logic-based model of pathological mechanisms, kali searches for therapeutic targets able to reduce the reachability of the attractors associated with pathological phenotypes, thus reducing their likeliness. kali is illustrated on an example network and used on a biological case study. The case study is a published logic-based model of bladder tumorigenesis from which kali returns consistent results. However, like any computational tool, kali can predict but cannot replace human expertise: it is a supporting tool for coping with the complexity of biological systems in the field of drug discovery. PMID:29515890

Generalization and capacity of extensively large two-layered perceptrons.

PubMed

Rosen-Zvi, Michal; Engel, Andreas; Kanter, Ido

2002-09-01

The generalization ability and storage capacity of a treelike two-layered neural network with a number of hidden units scaling as the input dimension is examined. The mapping from the input to the hidden layer is via Boolean functions; the mapping from the hidden layer to the output is done by a perceptron. The analysis is within the replica framework where an order parameter characterizing the overlap between two networks in the combined space of Boolean functions and hidden-to-output couplings is introduced. The maximal capacity of such networks is found to scale linearly with the logarithm of the number of Boolean functions per hidden unit. The generalization process exhibits a first-order phase transition from poor to perfect learning for the case of discrete hidden-to-output couplings. The critical number of examples per input dimension, alpha(c), at which the transition occurs, again scales linearly with the logarithm of the number of Boolean functions. In the case of continuous hidden-to-output couplings, the generalization error decreases according to the same power law as for the perceptron, with the prefactor being different.

Boolean and brain-inspired computing using spin-transfer torque devices

NASA Astrophysics Data System (ADS)

Fan, Deliang

Several completely new approaches (such as spintronic, carbon nanotube, graphene, TFETs, etc.) to information processing and data storage technologies are emerging to address the time frame beyond current Complementary Metal-Oxide-Semiconductor (CMOS) roadmap. The high speed magnetization switching of a nano-magnet due to current induced spin-transfer torque (STT) have been demonstrated in recent experiments. Such STT devices can be explored in compact, low power memory and logic design. In order to truly leverage STT devices based computing, researchers require a re-think of circuit, architecture, and computing model, since the STT devices are unlikely to be drop-in replacements for CMOS. The potential of STT devices based computing will be best realized by considering new computing models that are inherently suited to the characteristics of STT devices, and new applications that are enabled by their unique capabilities, thereby attaining performance that CMOS cannot achieve. The goal of this research is to conduct synergistic exploration in architecture, circuit and device levels for Boolean and brain-inspired computing using nanoscale STT devices. Specifically, we first show that the non-volatile STT devices can be used in designing configurable Boolean logic blocks. We propose a spin-memristor threshold logic (SMTL) gate design, where memristive cross-bar array is used to perform current mode summation of binary inputs and the low power current mode spintronic threshold device carries out the energy efficient threshold operation. Next, for brain-inspired computing, we have exploited different spin-transfer torque device structures that can implement the hard-limiting and soft-limiting artificial neuron transfer functions respectively. We apply such STT based neuron (or 'spin-neuron') in various neural network architectures, such as hierarchical temporal memory and feed-forward neural network, for performing "human-like" cognitive computing, which show more than two orders of lower energy consumption compared to state of the art CMOS implementation. Finally, we show the dynamics of injection locked Spin Hall Effect Spin-Torque Oscillator (SHE-STO) cluster can be exploited as a robust multi-dimensional distance metric for associative computing, image/ video analysis, etc. Our simulation results show that the proposed system architecture with injection locked SHE-STOs and the associated CMOS interface circuits can be suitable for robust and energy efficient associative computing and pattern matching.

The Construction of 3-d Neutral Density for Arbitrary Data Sets

NASA Astrophysics Data System (ADS)

Riha, S.; McDougall, T. J.; Barker, P. M.

2014-12-01

The Neutral Density variable allows inference of water pathways from thermodynamic properties in the global ocean, and is therefore an essential component of global ocean circulation analysis. The widely used algorithm for the computation of Neutral Density yields accurate results for data sets which are close to the observed climatological ocean. Long-term numerical climate simulations, however, often generate a significant drift from present-day climate, which renders the existing algorithm inaccurate. To remedy this problem, new algorithms which operate on arbitrary data have been developed, which may potentially be used to compute Neutral Density during runtime of a numerical model.We review existing approaches for the construction of Neutral Density in arbitrary data sets, detail their algorithmic structure, and present an analysis of the computational cost for implementations on a single-CPU computer. We discuss possible strategies for the implementation in state-of-the-art numerical models, with a focus on distributed computing environments.

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming.

PubMed

Ostrowski, M; Paulevé, L; Schaub, T; Siegel, A; Guziolowski, C

2016-11-01

Boolean networks (and more general logic models) are useful frameworks to study signal transduction across multiple pathways. Logic models can be learned from a prior knowledge network structure and multiplex phosphoproteomics data. However, most efficient and scalable training methods focus on the comparison of two time-points and assume that the system has reached an early steady state. In this paper, we generalize such a learning procedure to take into account the time series traces of phosphoproteomics data in order to discriminate Boolean networks according to their transient dynamics. To that end, we identify a necessary condition that must be satisfied by the dynamics of a Boolean network to be consistent with a discretized time series trace. Based on this condition, we use Answer Set Programming to compute an over-approximation of the set of Boolean networks which fit best with experimental data and provide the corresponding encodings. Combined with model-checking approaches, we end up with a global learning algorithm. Our approach is able to learn logic models with a true positive rate higher than 78% in two case studies of mammalian signaling networks; for a larger case study, our method provides optimal answers after 7min of computation. We quantified the gain in our method predictions precision compared to learning approaches based on static data. Finally, as an application, our method proposes erroneous time-points in the time series data with respect to the optimal learned logic models. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Steady state analysis of Boolean molecular network models via model reduction and computational algebra.

PubMed

Veliz-Cuba, Alan; Aguilar, Boris; Hinkelmann, Franziska; Laubenbacher, Reinhard

2014-06-26

A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly popular modeling paradigm for networks lacking detailed kinetic information. For small models, the problem can be solved by exhaustive enumeration of all state transitions. But for larger models this is not feasible, since the size of the phase space grows exponentially with the dimension of the network. The dimension of published models is growing to over 100, so that efficient methods for steady state determination are essential. Several methods have been proposed for large networks, some of them heuristic. While these methods represent a substantial improvement in scalability over exhaustive enumeration, the problem for large networks is still unsolved in general. This paper presents an algorithm that consists of two main parts. The first is a graph theoretic reduction of the wiring diagram of the network, while preserving all information about steady states. The second part formulates the determination of all steady states of a Boolean network as a problem of finding all solutions to a system of polynomial equations over the finite number system with two elements. This problem can be solved with existing computer algebra software. This algorithm compares favorably with several existing algorithms for steady state determination. One advantage is that it is not heuristic or reliant on sampling, but rather determines algorithmically and exactly all steady states of a Boolean network. The code for the algorithm, as well as the test suite of benchmark networks, is available upon request from the corresponding author. The algorithm presented in this paper reliably determines all steady states of sparse Boolean networks with up to 1000 nodes. The algorithm is effective at analyzing virtually all published models even those of moderate connectivity. The problem for large Boolean networks with high average connectivity remains an open problem.

Steady state analysis of Boolean molecular network models via model reduction and computational algebra

PubMed Central

2014-01-01

Background A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly popular modeling paradigm for networks lacking detailed kinetic information. For small models, the problem can be solved by exhaustive enumeration of all state transitions. But for larger models this is not feasible, since the size of the phase space grows exponentially with the dimension of the network. The dimension of published models is growing to over 100, so that efficient methods for steady state determination are essential. Several methods have been proposed for large networks, some of them heuristic. While these methods represent a substantial improvement in scalability over exhaustive enumeration, the problem for large networks is still unsolved in general. Results This paper presents an algorithm that consists of two main parts. The first is a graph theoretic reduction of the wiring diagram of the network, while preserving all information about steady states. The second part formulates the determination of all steady states of a Boolean network as a problem of finding all solutions to a system of polynomial equations over the finite number system with two elements. This problem can be solved with existing computer algebra software. This algorithm compares favorably with several existing algorithms for steady state determination. One advantage is that it is not heuristic or reliant on sampling, but rather determines algorithmically and exactly all steady states of a Boolean network. The code for the algorithm, as well as the test suite of benchmark networks, is available upon request from the corresponding author. Conclusions The algorithm presented in this paper reliably determines all steady states of sparse Boolean networks with up to 1000 nodes. The algorithm is effective at analyzing virtually all published models even those of moderate connectivity. The problem for large Boolean networks with high average connectivity remains an open problem. PMID:24965213

Identification of Boolean Network Models From Time Series Data Incorporating Prior Knowledge.

PubMed

Leifeld, Thomas; Zhang, Zhihua; Zhang, Ping

2018-01-01

Motivation: Mathematical models take an important place in science and engineering. A model can help scientists to explain dynamic behavior of a system and to understand the functionality of system components. Since length of a time series and number of replicates is limited by the cost of experiments, Boolean networks as a structurally simple and parameter-free logical model for gene regulatory networks have attracted interests of many scientists. In order to fit into the biological contexts and to lower the data requirements, biological prior knowledge is taken into consideration during the inference procedure. In the literature, the existing identification approaches can only deal with a subset of possible types of prior knowledge. Results: We propose a new approach to identify Boolean networks from time series data incorporating prior knowledge, such as partial network structure, canalizing property, positive and negative unateness. Using vector form of Boolean variables and applying a generalized matrix multiplication called the semi-tensor product (STP), each Boolean function can be equivalently converted into a matrix expression. Based on this, the identification problem is reformulated as an integer linear programming problem to reveal the system matrix of Boolean model in a computationally efficient way, whose dynamics are consistent with the important dynamics captured in the data. By using prior knowledge the number of candidate functions can be reduced during the inference. Hence, identification incorporating prior knowledge is especially suitable for the case of small size time series data and data without sufficient stimuli. The proposed approach is illustrated with the help of a biological model of the network of oxidative stress response. Conclusions: The combination of efficient reformulation of the identification problem with the possibility to incorporate various types of prior knowledge enables the application of computational model inference to systems with limited amount of time series data. The general applicability of this methodological approach makes it suitable for a variety of biological systems and of general interest for biological and medical research.

Boolean and fuzzy logic implemented at the molecular level

NASA Astrophysics Data System (ADS)

Gentili, Pier Luigi

2007-07-01

In this work, it is shown how to implement both hard and soft computing by means of two structurally related heterocyclic compounds: flindersine (FL) and 6(5H)-phenanthridinone (PH). Since FL and PH have a carbonyl group in their molecular skeletons, they exhibit Proximity Effects in their photophysics. In other words, they have an emission power that can be modulated through external inputs such as temperature ( T) and hydrogen-bonding donation (HBD) ability of solvents. This phenomenology can be exploited to implement both crisp and fuzzy logic. Fuzzy Logic Systems (FLSs) wherein the antecedents of the rules are connected through the AND operator, are built by both the Mamdani's and Sugeno's models. Finally, they are adopted as approximators of the proximity effect phenomenon and tested for their prediction capabilities. Moreover, FL as photochromic compound is also a multiply configurable crisp logic molecular element.

Reconfigurable optical implementation of quantum complex networks

NASA Astrophysics Data System (ADS)

Nokkala, J.; Arzani, F.; Galve, F.; Zambrini, R.; Maniscalco, S.; Piilo, J.; Treps, N.; Parigi, V.

2018-05-01

Network theory has played a dominant role in understanding the structure of complex systems and their dynamics. Recently, quantum complex networks, i.e. collections of quantum systems arranged in a non-regular topology, have been theoretically explored leading to significant progress in a multitude of diverse contexts including, e.g., quantum transport, open quantum systems, quantum communication, extreme violation of local realism, and quantum gravity theories. Despite important progress in several quantum platforms, the implementation of complex networks with arbitrary topology in quantum experiments is still a demanding task, especially if we require both a significant size of the network and the capability of generating arbitrary topology—from regular to any kind of non-trivial structure—in a single setup. Here we propose an all optical and reconfigurable implementation of quantum complex networks. The experimental proposal is based on optical frequency combs, parametric processes, pulse shaping and multimode measurements allowing the arbitrary control of the number of the nodes (optical modes) and topology of the links (interactions between the modes) within the network. Moreover, we also show how to simulate quantum dynamics within the network combined with the ability to address its individual nodes. To demonstrate the versatility of these features, we discuss the implementation of two recently proposed probing techniques for quantum complex networks and structured environments.

Interpolation of the Extended Boolean Retrieval Model.

ERIC Educational Resources Information Center

Zanger, Daniel Z.

2002-01-01

Presents an interpolation theorem for an extended Boolean information retrieval model. Results show that whenever two or more documents are similarly ranked at any two points for a query containing exactly two terms, then they are similarly ranked at all points in between; and that results can fail for queries with more than two terms. (Author/LRW)

The Concept of the "Imploded Boolean Search": A Case Study with Undergraduate Chemistry Students

ERIC Educational Resources Information Center

Tomaszewski, Robert

2016-01-01

Critical thinking and analytical problem-solving skills in research involves using different search strategies. A proposed concept for an "Imploded Boolean Search" combines three unique identifiable field types to perform a search: keyword(s), numerical value(s), and a chemical structure or reaction. The object of this type of search is…

Energy and criticality in random Boolean networks

NASA Astrophysics Data System (ADS)

Andrecut, M.; Kauffman, S. A.

2008-06-01

The central issue of the research on the Random Boolean Networks (RBNs) model is the characterization of the critical transition between ordered and chaotic phases. Here, we discuss an approach based on the ‘energy’ associated with the unsatisfiability of the Boolean functions in the RBNs model, which provides an upper bound estimation for the energy used in computation. We show that in the ordered phase the RBNs are in a ‘dissipative’ regime, performing mostly ‘downhill’ moves on the ‘energy’ landscape. Also, we show that in the disordered phase the RBNs have to ‘hillclimb’ on the ‘energy’ landscape in order to perform computation. The analytical results, obtained using Derrida's approximation method, are in complete agreement with numerical simulations.

Optical programmable Boolean logic unit.

PubMed

Chattopadhyay, Tanay

2011-11-10

Logic units are the building blocks of many important computational operations likes arithmetic, multiplexer-demultiplexer, radix conversion, parity checker cum generator, etc. Multifunctional logic operation is very much essential in this respect. Here a programmable Boolean logic unit is proposed that can perform 16 Boolean logical operations from a single optical input according to the programming input without changing the circuit design. This circuit has two outputs. One output is complementary to the other. Hence no loss of data can occur. The circuit is basically designed by a 2×2 polarization independent optical cross bar switch. Performance of the proposed circuit has been achieved by doing numerical simulations. The binary logical states (0,1) are represented by the absence of light (null) and presence of light, respectively.

Scheme for Implementing Teleporting an Arbitrary Tripartite Entangled State in Cavity QED

NASA Astrophysics Data System (ADS)

Wang, Xue-Wen; Peng, Zhao-Hui

2009-10-01

We propose to teleport an arbitrary tripartite entangled state in cavity QED. In this scheme, the five-qubit Brown state is chosen as the quantum channel. It has been shown that the teleportation protocol can be completed perfectly with two different measurement methods. In the future, our scheme might be realizable based on present experimental technology.

BEM for wave equation with boundary in arbitrary motion and applications to compressible potential aerodynamics of airplanes and helicopters

NASA Technical Reports Server (NTRS)

Morino, Luigi; Bharadvaj, Bala K.; Freedman, Marvin I.; Tseng, Kadin

1988-01-01

The wave equation for an object in arbitrary motion is investigated analytically using a BEM approach, and practical applications to potential flows of compressible fluids around aircraft wings and helicopter rotors are considered. The treatment accounts for arbitrary combined rotational and translational motion of the reference frame and for the wake motion. The numerical implementation as a computer algorithm is demonstrated on problems with prescribed and free wakes, the former in compressible flows and the latter for incompressible flows; results are presented graphically and briefly characterized.

Efficient G(sup 4)FET-Based Logic Circuits

NASA Technical Reports Server (NTRS)

Vatan, Farrokh

2008-01-01

A total of 81 optimal logic circuits based on four-gate field-effect transistors (G(sup 4)4FETs) have been designed to implement all Boolean functions of up to three variables. The purpose of this development was to lend credence to the expectation that logic circuits based on G(sup 4)FETs could be more efficient (in the sense that they could contain fewer transistors), relative to functionally equivalent logic circuits based on conventional transistors. A G(sup 4)FET a combination of a junction field-effect transistor (JFET) and a metal oxide/semiconductor field-effect transistor (MOSFET) superimposed in a single silicon island and can therefore be regarded as two transistors sharing the same body. A G(sup 4)FET can also be regarded as a single device having four gates: two side junction-based gates, a top MOS gate, and a back gate activated by biasing of a silicon-on-insulator substrate. Each of these gates can be used to control the conduction characteristics of the transistor; this possibility creates new options for designing analog, radio-frequency, mixed-signal, and digital circuitry. One such option is to design a G(sup 4)FET to function as a three-input NOT-majority gate, which has been shown to be a universal and programmable logic gate. Optimal NOT-majority-gate, G(sup 4)FET-based logic-circuit designs were obtained in a comparative study that also included formulation of functionally equivalent logic circuits based on NOR and NAND gates implemented by use of conventional transistors. In the study, the problem of finding the optimal design for each logic function and each transistor type was solved as an integer-programming optimization problem. Considering all 81 non-equivalent Boolean functions included in the study, it was found that in 63% of the cases, fewer logic gates (and, hence, fewer transistors) would be needed in the G(sup 4)FET-based implementations.

Designing Networks that are Capable of Self-Healing and Adapting

DTIC Science & Technology

2017-04-01

from statistical mechanics, combinatorics, boolean networks, and numerical simulations, and inspired by design principles from biological networks, we... principles for self-healing networks, and applications, and construct an all-possible-paths model for network adaptation. 2015-11-16 UNIT CONVERSION...combinatorics, boolean networks, and numerical simulations, and inspired by design principles from biological networks, we will undertake the fol

Equilibrium and nonequilibrium properties of Boolean decision problems on scale-free graphs with competing interactions with external biases

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Andresen, Juan Carlos; Janzen, Katharina; Katzgraber, Helmut G.

2013-03-01

We study the equilibrium and nonequilibrium properties of Boolean decision problems with competing interactions on scale-free graphs in a magnetic field. Previous studies at zero field have shown a remarkable equilibrium stability of Boolean variables (Ising spins) with competing interactions (spin glasses) on scale-free networks. When the exponent that describes the power-law decay of the connectivity of the network is strictly larger than 3, the system undergoes a spin-glass transition. However, when the exponent is equal to or less than 3, the glass phase is stable for all temperatures. First we perform finite-temperature Monte Carlo simulations in a field to test the robustness of the spin-glass phase and show, in agreement with analytical calculations, that the system exhibits a de Almeida-Thouless line. Furthermore, we study avalanches in the system at zero temperature to see if the system displays self-organized criticality. This would suggest that damage (avalanches) can spread across the whole system with nonzero probability, i.e., that Boolean decision problems on scale-free networks with competing interactions are fragile when not in thermal equilibrium.

Wave Field Synthesis of moving sources with arbitrary trajectory and velocity profile.

PubMed

Firtha, Gergely; Fiala, Péter

2017-08-01

The sound field synthesis of moving sound sources is of great importance when dynamic virtual sound scenes are to be reconstructed. Previous solutions considered only virtual sources moving uniformly along a straight trajectory, synthesized employing a linear loudspeaker array. This article presents the synthesis of point sources following an arbitrary trajectory. Under high-frequency assumptions 2.5D Wave Field Synthesis driving functions are derived for arbitrary shaped secondary source contours by adapting the stationary phase approximation to the dynamic description of sources in motion. It is explained how a referencing function should be chosen in order to optimize the amplitude of synthesis on an arbitrary receiver curve. Finally, a finite difference implementation scheme is considered, making the presented approach suitable for real-time applications.

Recurrent-neural-network-based Boolean factor analysis and its application to word clustering.

PubMed

Frolov, Alexander A; Husek, Dusan; Polyakov, Pavel Yu

2009-07-01

The objective of this paper is to introduce a neural-network-based algorithm for word clustering as an extension of the neural-network-based Boolean factor analysis algorithm (Frolov , 2007). It is shown that this extended algorithm supports even the more complex model of signals that are supposed to be related to textual documents. It is hypothesized that every topic in textual data is characterized by a set of words which coherently appear in documents dedicated to a given topic. The appearance of each word in a document is coded by the activity of a particular neuron. In accordance with the Hebbian learning rule implemented in the network, sets of coherently appearing words (treated as factors) create tightly connected groups of neurons, hence, revealing them as attractors of the network dynamics. The found factors are eliminated from the network memory by the Hebbian unlearning rule facilitating the search of other factors. Topics related to the found sets of words can be identified based on the words' semantics. To make the method complete, a special technique based on a Bayesian procedure has been developed for the following purposes: first, to provide a complete description of factors in terms of component probability, and second, to enhance the accuracy of classification of signals to determine whether it contains the factor. Since it is assumed that every word may possibly contribute to several topics, the proposed method might be related to the method of fuzzy clustering. In this paper, we show that the results of Boolean factor analysis and fuzzy clustering are not contradictory, but complementary. To demonstrate the capabilities of this attempt, the method is applied to two types of textual data on neural networks in two different languages. The obtained topics and corresponding words are at a good level of agreement despite the fact that identical topics in Russian and English conferences contain different sets of keywords.

Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape

PubMed Central

Aldana, Maximino; Benítez, Mariana; Cortes-Poza, Yuriria; Espinosa-Soto, Carlos; Hartasánchez, Diego A.; Lotto, R. Beau; Malkin, David; Escalera Santos, Gerardo J.; Padilla-Longoria, Pablo

2008-01-01

In contrast to the classical view of development as a preprogrammed and deterministic process, recent studies have demonstrated that stochastic perturbations of highly non-linear systems may underlie the emergence and stability of biological patterns. Herein, we address the question of whether noise contributes to the generation of the stereotypical temporal pattern in gene expression during flower development. We modeled the regulatory network of organ identity genes in the Arabidopsis thaliana flower as a stochastic system. This network has previously been shown to converge to ten fixed-point attractors, each with gene expression arrays that characterize inflorescence cells and primordial cells of sepals, petals, stamens, and carpels. The network used is binary, and the logical rules that govern its dynamics are grounded in experimental evidence. We introduced different levels of uncertainty in the updating rules of the network. Interestingly, for a level of noise of around 0.5–10%, the system exhibited a sequence of transitions among attractors that mimics the sequence of gene activation configurations observed in real flowers. We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model. Interestingly, the Glass dynamics recover a temporal sequence of attractors, that is qualitatively similar, although not identical, to that obtained using the Boolean model. Thus, time ordering in the emergence of cell-fate patterns is not an artifact of synchronous updating in the Boolean model. Therefore, our model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification. It also constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of cells with different genetic configurations during development. PMID:18978941

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

Rivera-Durón, R. R., E-mail: roberto.rivera@ipicyt.edu.mx; Campos-Cantón, E., E-mail: eric.campos@ipicyt.edu.mx; Campos-Cantón, I.

We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enablemore » future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.« less

Stabilizing Motifs in Autonomous Boolean Networks and the Yeast Cell Cycle Oscillator

NASA Astrophysics Data System (ADS)

Sevim, Volkan; Gong, Xinwei; Socolar, Joshua

2009-03-01

Synchronously updated Boolean networks are widely used to model gene regulation. Some properties of these model networks are known to be artifacts of the clocking in the update scheme. Autonomous updating is a less artificial scheme that allows one to introduce small timing perturbations and study stability of the attractors. We argue that the stabilization of a limit cycle in an autonomous Boolean network requires a combination of motifs such as feed-forward loops and auto-repressive links that can correct small fluctuations in the timing of switching events. A recently published model of the transcriptional cell-cycle oscillator in yeast contains the motifs necessary for stability under autonomous updating [1]. [1] D. A. Orlando, et al. Nature (London), 4530 (7197):0 944--947, 2008.

Towards Symbolic Model Checking for Multi-Agent Systems via OBDDs

NASA Technical Reports Server (NTRS)

Raimondi, Franco; Lomunscio, Alessio

2004-01-01

We present an algorithm for model checking temporal-epistemic properties of multi-agent systems, expressed in the formalism of interpreted systems. We first introduce a technique for the translation of interpreted systems into boolean formulae, and then present a model-checking algorithm based on this translation. The algorithm is based on OBDD's, as they offer a compact and efficient representation for boolean formulae.

Feedback Controller Design for the Synchronization of Boolean Control Networks.

PubMed

Liu, Yang; Sun, Liangjie; Lu, Jianquan; Liang, Jinling

2016-09-01

This brief investigates the partial and complete synchronization of two Boolean control networks (BCNs). Necessary and sufficient conditions for partial and complete synchronization are established by the algebraic representations of logical dynamics. An algorithm is obtained to construct the feedback controller that guarantees the synchronization of master and slave BCNs. Two biological examples are provided to illustrate the effectiveness of the obtained results.

Computer Aided Instruction for a Course in Boolean Algebra and Logic Design. Final Report (Revised).

ERIC Educational Resources Information Center

Roy, Rob

The use of computers to prepare deficient college and graduate students for courses that build upon previously acquired information would solve the growing problem of professors who must spend up to one third of their class time in review of material. But examination of students who were taught Boolean Algebra and Logic Design by means of Computer…

Three-dimensional zonal grids about arbitrary shapes by Poisson's equation

NASA Technical Reports Server (NTRS)

Sorenson, Reese L.

1988-01-01

A method for generating 3-D finite difference grids about or within arbitrary shapes is presented. The 3-D Poisson equations are solved numerically, with values for the inhomogeneous terms found automatically by the algorithm. Those inhomogeneous terms have the effect near boundaries of reducing cell skewness and imposing arbitrary cell height. The method allows the region of interest to be divided into zones (blocks), allowing the method to be applicable to almost any physical domain. A FORTRAN program called 3DGRAPE has been written to implement the algorithm. Lastly, a method for redistributing grid points along lines normal to boundaries will be described.

Deriving Laws from Ordering Relations

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.

2003-01-01

It took much effort in the early days of non-Euclidean geometry to break away from the mindset that all spaces are flat and that two distinct parallel lines do not cross. Up to that point, all that was known was Euclidean geometry, and it was difficult to imagine anything else. We have suffered a similar handicap brought on by the enormous relevance of Boolean algebra to the problems of our age-logic and set theory. Previously, I demonstrated that the algebra of questions is not Boolean, but rather is described by the free distributive algebra. To get to this stage took much effort, as many obstacles-most self-placed-had to be overcome. As Boolean algebras were all I had ever known, it was almost impossible for me to imagine working with an algebra where elements do not have complements. With this realization, it became very clear that the sum and product rules of probability theory at the most basic level had absolutely nothing to do with the Boolean algebra of logical statements. Instead, a measure of degree of inclusion can be invented for many different partially ordered sets, and the sum and product rules fall out of the associativity and distributivity of the algebra. To reinforce this very important idea, this paper will go over how these constructions are made, while focusing on the underlying assumptions. I will derive the sum and product rules for a distributive lattice in general and demonstrate how this leads to probability theory on the Boolean lattice and is related to the calculus of quantum mechanical amplitudes on the partially ordered set of experimental setups. I will also discuss the rules that can be derived from modular lattices and their relevance to the cross-ratio of projective geometry.

Identification of control targets in Boolean molecular network models via computational algebra.

PubMed

Murrugarra, David; Veliz-Cuba, Alan; Aguilar, Boris; Laubenbacher, Reinhard

2016-09-23

Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network. Supplementary data is available online and our code in Macaulay2 and Matlab are available via http://www.ms.uky.edu/~dmu228/ControlAlg . This paper presents a novel method for the identification of intervention targets in Boolean network models. The results in this paper show that the proposed methods are useful and efficient for moderately large networks.

The computational core and fixed point organization in Boolean networks

NASA Astrophysics Data System (ADS)

Correale, L.; Leone, M.; Pagnani, A.; Weigt, M.; Zecchina, R.

2006-03-01

In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows us to prune simple logical cascades and underdetermined variables, returning thereby the computational core of the network. Second, we apply the cavity method to analyse the number and organization of fixed points. We find in particular a phase transition between an easy and a complex regulatory phase, the latter being characterized by the existence of an exponential number of macroscopically separated fixed point clusters. The different techniques developed are reinterpreted as algorithms for the analysis of single Boolean networks, and they are applied in the analysis of and in silico experiments on the gene regulatory networks of baker's yeast (Saccharomyces cerevisiae) and the segment-polarity genes of the fruitfly Drosophila melanogaster.

Observability of Boolean multiplex control networks

NASA Astrophysics Data System (ADS)

Wu, Yuhu; Xu, Jingxue; Sun, Xi-Ming; Wang, Wei

2017-04-01

Boolean multiplex (multilevel) networks (BMNs) are currently receiving considerable attention as theoretical arguments for modeling of biological systems and system level analysis. Studying control-related problems in BMNs may not only provide new views into the intrinsic control in complex biological systems, but also enable us to develop a method for manipulating biological systems using exogenous inputs. In this article, the observability of the Boolean multiplex control networks (BMCNs) are studied. First, the dynamical model and structure of BMCNs with control inputs and outputs are constructed. By using of Semi-Tensor Product (STP) approach, the logical dynamics of BMCNs is converted into an equivalent algebraic representation. Then, the observability of the BMCNs with two different kinds of control inputs is investigated by giving necessary and sufficient conditions. Finally, examples are given to illustrate the efficiency of the obtained theoretical results.

Boolean network representation of contagion dynamics during a financial crisis

NASA Astrophysics Data System (ADS)

Caetano, Marco Antonio Leonel; Yoneyama, Takashi

2015-01-01

This work presents a network model for representation of the evolution of certain patterns of economic behavior. More specifically, after representing the agents as points in a space in which each dimension associated to a relevant economic variable, their relative "motions" that can be either stationary or discordant, are coded into a boolean network. Patterns with stationary averages indicate the maintenance of status quo, whereas discordant patterns represent aggregation of new agent into the cluster or departure from the former policies. The changing patterns can be embedded into a network representation, particularly using the concept of autocatalytic boolean networks. As a case study, the economic tendencies of the BRIC countries + Argentina were studied. Although Argentina is not included in the cluster formed by BRIC countries, it tends to follow the BRIC members because of strong commercial ties.

Modeling stochasticity and robustness in gene regulatory networks.

PubMed

Garg, Abhishek; Mohanram, Kartik; Di Cara, Alessandro; De Micheli, Giovanni; Xenarios, Ioannis

2009-06-15

Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed interest in Boolean modeling techniques for gene regulatory networks (GRNs). However, due to their deterministic nature, it is often difficult to identify whether these modeling approaches are robust to the addition of stochastic noise that is widespread in gene regulatory processes. Stochasticity in Boolean models of GRNs has been addressed relatively sparingly in the past, mainly by flipping the expression of genes between different expression levels with a predefined probability. This stochasticity in nodes (SIN) model leads to over representation of noise in GRNs and hence non-correspondence with biological observations. In this article, we introduce the stochasticity in functions (SIF) model for simulating stochasticity in Boolean models of GRNs. By providing biological motivation behind the use of the SIF model and applying it to the T-helper and T-cell activation networks, we show that the SIF model provides more biologically robust results than the existing SIN model of stochasticity in GRNs. Algorithms are made available under our Boolean modeling toolbox, GenYsis. The software binaries can be downloaded from http://si2.epfl.ch/ approximately garg/genysis.html.

Discrete interference modeling via boolean algebra.

PubMed

Beckhoff, Gerhard

2011-01-01

Two types of boolean functions are considered, the locus function of n variables, and the interval function of ν = n - 1 variables. A 1-1 mapping is given that takes elements (cells) of the interval function to antidual pairs of elements in the locus function, and vice versa. A set of ν binary codewords representing the intervals are defined and used to generate the codewords of all genomic regions. Next a diallelic three-point system is reviewed in the light of boolean functions, which leads to redefining complete interference by a logic function. Together with the upper bound of noninterference already defined by a boolean function, it confines the region of interference. Extensions of these two functions to any finite number of ν are straightforward, but have been also made in terms of variables taken from the inclusion-exclusion principle (expressing "at least" and "exactly equal to" a decimal integer). Two coefficients of coincidence for systems with more than three loci are defined and discussed, one using the average of several individual coefficients and the other taking as coefficient a real number between zero and one. Finally, by way of a malfunction of the mod-2 addition, it is shown that a four-point system may produce two different functions, one of which exhibiting loss of a class of odd recombinants.

Boolean decision problems with competing interactions on scale-free networks: Equilibrium and nonequilibrium behavior in an external bias

NASA Astrophysics Data System (ADS)

Zhu, Zheng; Andresen, Juan Carlos; Moore, M. A.; Katzgraber, Helmut G.

2014-02-01

We study the equilibrium and nonequilibrium properties of Boolean decision problems with competing interactions on scale-free networks in an external bias (magnetic field). Previous studies at zero field have shown a remarkable equilibrium stability of Boolean variables (Ising spins) with competing interactions (spin glasses) on scale-free networks. When the exponent that describes the power-law decay of the connectivity of the network is strictly larger than 3, the system undergoes a spin-glass transition. However, when the exponent is equal to or less than 3, the glass phase is stable for all temperatures. First, we perform finite-temperature Monte Carlo simulations in a field to test the robustness of the spin-glass phase and show that the system has a spin-glass phase in a field, i.e., exhibits a de Almeida-Thouless line. Furthermore, we study avalanche distributions when the system is driven by a field at zero temperature to test if the system displays self-organized criticality. Numerical results suggest that avalanches (damage) can spread across the whole system with nonzero probability when the decay exponent of the interaction degree is less than or equal to 2, i.e., that Boolean decision problems on scale-free networks with competing interactions can be fragile when not in thermal equilibrium.

MO-FG-BRA-04: A Novel Time Weighted Density Correction for Stereotactic Lung Radiotherapy: A Phantom Study

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

Mohatt, D; Malhotra, H

Purpose: Conventional treatment plans for lung radiotherapy are created using either the free breathing (FB) scheme which represents the tumor at an arbitrary breathing phase of the patient’s respiratory cycle, or the average computed tomography (ACT) intensity projection over 10-binned phases. Neither method is entirely accurate because of the absence of time dependence of tumor movement. In the present “Hybrid” method, the HU of tumor in 3D space is determined by relative weighting of the HU of the tumor and lung in proportion to the time they spend at that location during the entire breathing cycle. Methods: A Quasar respiratorymore » motion phantom was employed to simulate lung tumor movement. Utilizing 4DCT image scans, volumetric modulated arc therapy (VMAT) plans were generated for three treatment planning scenarios which included conventional FB and ACT schemes, along with a third alternative Hybrid approach. Our internal target volume (ITV) hybrid structure was created using Boolean operation in Eclipse (ver. 11) treatment planning system, where independent sub-regions created by the gross tumor volume (GTV) overlap from the 10 motion phases were each assigned a time weighted CT value. The dose-volume-histograms (DVH) for each scheme were compared and analyzed. Results: Using our hybrid technique, we have demonstrated a reduction of 1.9% – 3.4% in total monitor units with respect to conventional treatment planning strategies, along with a 6 fold improvement in high dose spillage over the FB plan. The higher density ACT and Hybrid schemes also produced a slight enhancement in target conformity and reduction in low dose spillage. Conclusion: All treatment plans created in this study exceeded RTOG protocol criteria. Our results determine the free breathing approach yields an inaccurate account of the target treatment density. A significant decrease in unnecessary lung irradiation can be achieved by implementing Hybrid HU method with ACT method second best.« less

A representational basis for the development of a distributed expert system for Space Shuttle flight control

NASA Technical Reports Server (NTRS)

Helly, J. J., Jr.; Bates, W. V.; Cutler, M.; Kelem, S.

1984-01-01

A new representation of malfunction procedure logic which permits the automation of these procedures using Boolean normal forms is presented. This representation is discussed in the context of the development of an expert system for space shuttle flight control including software and hardware implementation modes, and a distributed architecture. The roles and responsibility of the flight control team as well as previous work toward the development of expert systems for flight control support at Johnson Space Center are discussed. The notion of malfunction procedures as graphs is introduced as well as the concept of hardware-equivalence.

Nonlinear dynamics based digital logic and circuits.

PubMed

Kia, Behnam; Lindner, John F; Ditto, William L

2015-01-01

We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two.

The Design and Implementation of a Translator for Arithmetic and Boolean Expressions.

DTIC Science & Technology

1980-01-01

fault toleranc- P-or imTarop-r token.- or incorrect tok- n or(I-r. F C icD - MUS" hc-IV CnP 2J n,-)2ri 9 Iot t rq 3C003 G~T. 3OD 0L 3COC~ 5G F. 30005 ... 30005 .GE. ph 50015 60. C 30006 .LE. DP 50016 61. C RELPNT-INTEGER, POINTER TO ENTRIES IN RELOPS ARRAYY 62. C TEMP -INTEGER, USED FOR DETERMINING IF...30002, 50012, 30003, 50013, 30004, 50014, 30005 , 50015, 71. 1 30006, 50016/, SUB/50006/, THEN/142408/ 72. C 73. C ******** EXECUTABLE CODE******** 74

The CADSS design automation system. [computerized design language for small digital systems

NASA Technical Reports Server (NTRS)

Franke, E. A.

1973-01-01

This research was designed to implement and extend a previously defined design automation system for the design of small digital structures. A description is included of the higher level language developed to describe systems as a sequence of register transfer operations. The system simulator which is used to determine if the original description is correct is also discussed. The design automation system produces tables describing the state transistions of the system and the operation of all registers. In addition all Boolean equations specifying system operation are minimized and converted to NAND gate structures. Suggestions for further extensions to the system are also given.

Quantum design rules for single molecule logic gates.

PubMed

Renaud, N; Hliwa, M; Joachim, C

2011-08-28

Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.

Multistate Memristive Tantalum Oxide Devices for Ternary Arithmetic

PubMed Central

Kim, Wonjoo; Chattopadhyay, Anupam; Siemon, Anne; Linn, Eike; Waser, Rainer; Rana, Vikas

2016-01-01

Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations. We demonstrate that multistate devices not only reduce the storage area consumption drastically, but also enable novel in-memory operations, such as computing using high-radix number systems, which could not be implemented using two-state devices. The use of high radix number system reduces the computational complexity by reducing the number of needed digits. Thus the number of calculation operations in an addition and the number of logic devices can be reduced. PMID:27834352

Multistate Memristive Tantalum Oxide Devices for Ternary Arithmetic.

PubMed

Kim, Wonjoo; Chattopadhyay, Anupam; Siemon, Anne; Linn, Eike; Waser, Rainer; Rana, Vikas

2016-11-11

Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations. We demonstrate that multistate devices not only reduce the storage area consumption drastically, but also enable novel in-memory operations, such as computing using high-radix number systems, which could not be implemented using two-state devices. The use of high radix number system reduces the computational complexity by reducing the number of needed digits. Thus the number of calculation operations in an addition and the number of logic devices can be reduced.

Communication Policies in Knowledge Networks

NASA Astrophysics Data System (ADS)

Ioannidis, Evangelos; Varsakelis, Nikos; Antoniou, Ioannis

2018-02-01

Faster knowledge attainment within organizations leads to improved innovation, and therefore competitive advantage. Interventions on the organizational network may be risky or costly or time-demanding. We investigate several communication policies in knowledge networks, which reduce the knowledge attainment time without interventions. We examine the resulting knowledge dynamics for real organizational networks, as well as for artificial networks. More specifically, we investigate the dependence of knowledge dynamics on: (1) the Selection Rule of agents for knowledge acquisition, and (2) the Order of implementation of "Selection" and "Filtering". Significant decrease of the knowledge attainment time (up to -74%) can be achieved by: (1) selecting agents of both high knowledge level and high knowledge transfer efficiency, and (2) implementing "Selection" after "Filtering" in contrast to the converse, implicitly assumed, conventional prioritization. The Non-Commutativity of "Selection" and "Filtering", reveals a Non-Boolean Logic of the Network Operations. The results demonstrate that significant improvement of knowledge dynamics can be achieved by implementing "fruitful" communication policies, by raising the awareness of agents, without any intervention on the network structure.

Multistate Memristive Tantalum Oxide Devices for Ternary Arithmetic

NASA Astrophysics Data System (ADS)

Kim, Wonjoo; Chattopadhyay, Anupam; Siemon, Anne; Linn, Eike; Waser, Rainer; Rana, Vikas

2016-11-01

Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations. We demonstrate that multistate devices not only reduce the storage area consumption drastically, but also enable novel in-memory operations, such as computing using high-radix number systems, which could not be implemented using two-state devices. The use of high radix number system reduces the computational complexity by reducing the number of needed digits. Thus the number of calculation operations in an addition and the number of logic devices can be reduced.

Does Sleep Improve Your Grammar? Preferential Consolidation of Arbitrary Components of New Linguistic Knowledge

PubMed Central

Mirković, Jelena; Gaskell, M. Gareth

2016-01-01

We examined the role of sleep-related memory consolidation processes in learning new form-meaning mappings. Specifically, we examined a Complementary Learning Systems account, which implies that sleep-related consolidation should be more beneficial for new hippocampally dependent arbitrary mappings (e.g. new vocabulary items) relative to new systematic mappings (e.g. grammatical regularities), which can be better encoded neocortically. The hypothesis was tested using a novel language with an artificial grammatical gender system. Stem-referent mappings implemented arbitrary aspects of the new language, and determiner/suffix+natural gender mappings implemented systematic aspects (e.g. tib scoiffesh + ballerina, tib mofeem + bride; ked jorool + cowboy, ked heefaff + priest). Importantly, the determiner-gender and the suffix-gender mappings varied in complexity and salience, thus providing a range of opportunities to detect beneficial effects of sleep for this type of mapping. Participants were trained on the new language using a word-picture matching task, and were tested after a 2-hour delay which included sleep or wakefulness. Participants in the sleep group outperformed participants in the wake group on tests assessing memory for the arbitrary aspects of the new mappings (individual vocabulary items), whereas we saw no evidence of a sleep benefit in any of the tests assessing memory for the systematic aspects of the new mappings: Participants in both groups extracted the salient determiner-natural gender mapping, but not the more complex suffix-natural gender mapping. The data support the predictions of the complementary systems account and highlight the importance of the arbitrariness/systematicity dimension in the consolidation process for declarative memories. PMID:27046022

Artificial neural networks using complex numbers and phase encoded weights.

PubMed

Michel, Howard E; Awwal, Abdul Ahad S

2010-04-01

The model of a simple perceptron using phase-encoded inputs and complex-valued weights is proposed. The aggregation function, activation function, and learning rule for the proposed neuron are derived and applied to Boolean logic functions and simple computer vision tasks. The complex-valued neuron (CVN) is shown to be superior to traditional perceptrons. An improvement of 135% over the theoretical maximum of 104 linearly separable problems (of three variables) solvable by conventional perceptrons is achieved without additional logic, neuron stages, or higher order terms such as those required in polynomial logic gates. The application of CVN in distortion invariant character recognition and image segmentation is demonstrated. Implementation details are discussed, and the CVN is shown to be very attractive for optical implementation since optical computations are naturally complex. The cost of the CVN is less in all cases than the traditional neuron when implemented optically. Therefore, all the benefits of the CVN can be obtained without additional cost. However, on those implementations dependent on standard serial computers, CVN will be more cost effective only in those applications where its increased power can offset the requirement for additional neurons.

Exact Algorithms for Output Encoding, State Assignment and Four-Level Boolean Minimization

DTIC Science & Technology

1989-10-01

APPROVED FOR PUBLIC DISTRIBUTION • DTIC MASSACHUSETTS INTITUTE OF TECHNOLOGY M VLSI PUBLICATIONSJAN 17 1990 VLSI Memo No. 89-569 JN. 9October 1989...nunijize large funclions exacly within reasonable amocunt. of CPt targeting twro-level logic imnplemientations involve finding ap- time. However, thle ,, m ...0(NV!) m ~iimizations . n5 10 The inptut encoding problemt can be exactly solved using mrultiple-valued Boolean nimuization. We present an exact (a) (b

A single-layer platform for Boolean logic and arithmetic through DNA excision in mammalian cells

PubMed Central

Weinberg, Benjamin H.; Hang Pham, N. T.; Caraballo, Leidy D.; Lozanoski, Thomas; Engel, Adrien; Bhatia, Swapnil; Wong, Wilson W.

2017-01-01

Genetic circuits engineered for mammalian cells often require extensive fine-tuning to perform their intended functions. To overcome this problem, we present a generalizable biocomputing platform that can engineer genetic circuits which function in human cells with minimal optimization. We used our Boolean Logic and Arithmetic through DNA Excision (BLADE) platform to build more than 100 multi-input-multi-output circuits. We devised a quantitative metric to evaluate the performance of the circuits in human embryonic kidney and Jurkat T cells. Of 113 circuits analysed, 109 functioned (96.5%) with the correct specified behavior without any optimization. We used our platform to build a three-input, two-output Full Adder and six-input, one-output Boolean Logic Look Up Table. We also used BLADE to design circuits with temporal small molecule-mediated inducible control and circuits that incorporate CRISPR/Cas9 to regulate endogenous mammalian genes. PMID:28346402

Constraint-Based Abstract Semantics for Temporal Logic: A Direct Approach to Design and Implementation

NASA Astrophysics Data System (ADS)

Banda, Gourinath; Gallagher, John P.

interpretation provides a practical approach to verifying properties of infinite-state systems. We apply the framework of abstract interpretation to derive an abstract semantic function for the modal μ-calculus, which is the basis for abstract model checking. The abstract semantic function is constructed directly from the standard concrete semantics together with a Galois connection between the concrete state-space and an abstract domain. There is no need for mixed or modal transition systems to abstract arbitrary temporal properties, as in previous work in the area of abstract model checking. Using the modal μ-calculus to implement CTL, the abstract semantics gives an over-approximation of the set of states in which an arbitrary CTL formula holds. Then we show that this leads directly to an effective implementation of an abstract model checking algorithm for CTL using abstract domains based on linear constraints. The implementation of the abstract semantic function makes use of an SMT solver. We describe an implemented system for proving properties of linear hybrid automata and give some experimental results.

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.

Optical Neural Classification Of Binary Patterns

NASA Astrophysics Data System (ADS)

Gustafson, Steven C.; Little, Gordon R.

1988-05-01

Binary pattern classification that may be implemented using optical hardware and neural network algorithms is considered. Pattern classification problems that have no concise description (as in classifying handwritten characters) or no concise computation (as in NP-complete problems) are expected to be particularly amenable to this approach. For example, optical processors that efficiently classify binary patterns in accordance with their Boolean function complexity might be designed. As a candidate for such a design, an optical neural network model is discussed that is designed for binary pattern classification and that consists of an optical resonator with a dynamic multiplex-recorded reflection hologram and a phase conjugate mirror with thresholding and gain. In this model, learning or training examples of binary patterns may be recorded on the hologram such that one bit in each pattern marks the pattern class. Any input pattern, including one with an unknown class or marker bit, will be modified by a large number of parallel interactions with the reflection hologram and nonlinear mirror. After perhaps several seconds and 100 billion interactions, a steady-state pattern may develop with a marker bit that represents a minimum-Boolean-complexity classification of the input pattern. Computer simulations are presented that illustrate progress in understanding the behavior of this model and in developing a processor design that could have commanding and enduring performance advantages compared to current pattern classification techniques.

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

NASA Technical Reports Server (NTRS)

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Prescribed burning impact on forest soil properties--a Fuzzy Boolean Nets approach.

PubMed

Castro, Ana C Meira; Paulo Carvalho, Joao; Ribeiro, S

2011-02-01

The Portuguese northern forests are often and severely affected by wildfires during the Summer season. These occurrences significantly affect and negatively impact all ecosystems, namely soil, fauna and flora. In order to reduce the occurrences of natural wildfires, some measures to control the availability of fuel mass are regularly implemented. Those preventive actions concern mainly prescribed burnings and vegetation pruning. This work reports on the impact of a prescribed burning on several forest soil properties, namely pH, soil moisture, organic matter content and iron content, by monitoring the soil self-recovery capabilities during a one year span. The experiments were carried out in soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, Portugal, which was kept intact from prescribed burnings during a period of four years. Soil samples were collected from five plots at three different layers (0-3, 3-6 and 6-18) 1 day before prescribed fire and at regular intervals after the prescribed fire. This paper presents an approach where Fuzzy Boolean Nets (FBN) and Fuzzy reasoning are used to extract qualitative knowledge regarding the effect of prescribed fire burning on soil properties. FBN were chosen due to the scarcity on available quantitative data. The results showed that soil properties were affected by prescribed burning practice and were unable to recover their initial values after one year. Copyright © 2010 Elsevier Inc. All rights reserved.

A General Computational Approach for Magnetohydrodynamic Flows Using the CFX Code: Buoyant Flow Through a Vertical Square Channel

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

Di Piazza, Ivan; Buehler, Leo

2000-09-15

The buoyancy-driven magnetoconvection in the cross section of an infinitely long vertical square duct is investigated numerically using the CFX code package. The implementation of a magnetohydrodynamic (MHD) problem in CFX is discussed, with particular reference to the Lorentz forces and the electric potential boundary conditions for arbitrary electrical conductivity of the walls. The method proposed is general and applies to arbitrary geometries with an arbitrary orientation of the magnetic field. Results for fully developed flow under various thermal boundary conditions are compared with asymptotic analytical solutions. The comparison shows that the asymptotic analysis is confirmed for highly conducting wallsmore » as high velocity jets occur at the side walls. For weakly conducting walls, the side layers become more conducting than the side walls, and strong electric currents flow within these layers parallel to the magnetic field. As a consequence, the velocity jets are suppressed, and the core solution is only corrected by the viscous forces near the wall. The implementation of MHD in CFX is achieved.« less

Emergence of diversity in homogeneous coupled Boolean networks

NASA Astrophysics Data System (ADS)

Kang, Chris; Aguilar, Boris; Shmulevich, Ilya

2018-05-01

The origin of multicellularity in metazoa is one of the fundamental questions of evolutionary biology. We have modeled the generic behaviors of gene regulatory networks in isogenic cells as stochastic nonlinear dynamical systems—coupled Boolean networks with perturbation. Model simulations under a variety of dynamical regimes suggest that the central characteristic of multicellularity, permanent spatial differentiation (diversification), indeed can arise. Additionally, we observe that diversification is more likely to occur near the critical regime of Lyapunov stability.

Using Common Table Expressions to Build a Scalable Boolean Query Generator for Clinical Data Warehouses

PubMed Central

Harris, Daniel R.; Henderson, Darren W.; Kavuluru, Ramakanth; Stromberg, Arnold J.; Johnson, Todd R.

2015-01-01

We present a custom, Boolean query generator utilizing common-table expressions (CTEs) that is capable of scaling with big datasets. The generator maps user-defined Boolean queries, such as those interactively created in clinical-research and general-purpose healthcare tools, into SQL. We demonstrate the effectiveness of this generator by integrating our work into the Informatics for Integrating Biology and the Bedside (i2b2) query tool and show that it is capable of scaling. Our custom generator replaces and outperforms the default query generator found within the Clinical Research Chart (CRC) cell of i2b2. In our experiments, sixteen different types of i2b2 queries were identified by varying four constraints: date, frequency, exclusion criteria, and whether selected concepts occurred in the same encounter. We generated non-trivial, random Boolean queries based on these 16 types; the corresponding SQL queries produced by both generators were compared by execution times. The CTE-based solution significantly outperformed the default query generator and provided a much more consistent response time across all query types (M=2.03, SD=6.64 vs. M=75.82, SD=238.88 seconds). Without costly hardware upgrades, we provide a scalable solution based on CTEs with very promising empirical results centered on performance gains. The evaluation methodology used for this provides a means of profiling clinical data warehouse performance. PMID:25192572

Boolean Modeling of Neural Systems with Point-Process Inputs and Outputs. Part I: Theory and Simulations

PubMed Central

Marmarelis, Vasilis Z.; Zanos, Theodoros P.; Berger, Theodore W.

2010-01-01

This paper presents a new modeling approach for neural systems with point-process (spike) inputs and outputs that utilizes Boolean operators (i.e. modulo 2 multiplication and addition that correspond to the logical AND and OR operations respectively, as well as the AND_NOT logical operation representing inhibitory effects). The form of the employed mathematical models is akin to a “Boolean-Volterra” model that contains the product terms of all relevant input lags in a hierarchical order, where terms of order higher than first represent nonlinear interactions among the various lagged values of each input point-process or among lagged values of various inputs (if multiple inputs exist) as they reflect on the output. The coefficients of this Boolean-Volterra model are also binary variables that indicate the presence or absence of the respective term in each specific model/system. Simulations are used to explore the properties of such models and the feasibility of their accurate estimation from short data-records in the presence of noise (i.e. spurious spikes). The results demonstrate the feasibility of obtaining reliable estimates of such models, with excitatory and inhibitory terms, in the presence of considerable noise (spurious spikes) in the outputs and/or the inputs in a computationally efficient manner. A pilot application of this approach to an actual neural system is presented in the companion paper (Part II). PMID:19517238

Inferring Toxicological Responses of HepG2 Cells from ...

EPA Pesticide Factsheets

Understanding the dynamic perturbation of cell states by chemicals can aid in for predicting their adverse effects. High-content imaging (HCI) was used to measure the state of HepG2 cells over three time points (1, 24, and 72 h) in response to 976 ToxCast chemicals for 10 different concentrations (0.39-200µM). Cell state was characterized by p53 activation (p53), c-Jun activation (SK), phospho-Histone H2A.x (OS), phospho-Histone H3 (MA), alpha tubulin (Mt), mitochondrial membrane potential (MMP), mitochondrial mass (MM), cell cycle arrest (CCA), nuclear size (NS) and cell number (CN). Dynamic cell state perturbations due to each chemical concentration were utilized to infer coarse-grained dependencies between cellular functions as Boolean networks (BNs). BNs were inferred from data in two steps. First, the data for each state variable were discretized into changed/active (> 1 standard deviation), and unchanged/inactive values. Second, the discretized data were used to learn Boolean relationships between variables. In our case, a BN is a wiring diagram between nodes that represent 10 previously described observable phenotypes. Functional relationships between nodes were represented as Boolean functions. We found that inferred BN show that HepG2 cell response is chemical and concentration specific. We observed presence of both point and cycle BN attractors. In addition, there are instances where Boolean functions were not found. We believe that this may be either

Unidirectional Quantum Remote Control: Teleportation of Control-State

NASA Astrophysics Data System (ADS)

Zheng, Yi-Zhuang; Gu, Yong-Jian; Wu, Gui-Chu; Guo, Guang-Can

2003-08-01

We investigate the problem of teleportation of unitary operations by unidirectional control-state teleportation and propose a scheme called unidirectional quantum remote control. The scheme is based on the isomorphism between operation and state. It allows us to store a unitary operation in a control state, thereby teleportation of the unitary operation can be implemented by unidirectional teleportation of the control-state. We find that the probability of success for implementing an arbitrary unitary operation on arbitrary M-qubit state by unidirectional control-state teleportation is 4-M, and 2M ebits and 4M cbits are consumed in each teleportation. The project supported by the National Fundamental Research Programme (2001CB309300) and the Zhejiang Provincial Natural Science Foundation of China under Grant No. 102068

A simple method to derive bounds on the size and to train multilayer neural networks

NASA Technical Reports Server (NTRS)

Sartori, Michael A.; Antsaklis, Panos J.

1991-01-01

A new derivation is presented for the bounds on the size of a multilayer neural network to exactly implement an arbitrary training set; namely, the training set can be implemented with zero error with two layers and with the number of the hidden-layer neurons equal to no.1 is greater than p - 1. The derivation does not require the separation of the input space by particular hyperplanes, as in previous derivations. The weights for the hidden layer can be chosen almost arbitrarily, and the weights for the output layer can be found by solving no.1 + 1 linear equations. The method presented exactly solves (M), the multilayer neural network training problem, for any arbitrary training set.

Runtime Verification of C Programs

NASA Technical Reports Server (NTRS)

Havelund, Klaus

2008-01-01

We present in this paper a framework, RMOR, for monitoring the execution of C programs against state machines, expressed in a textual (nongraphical) format in files separate from the program. The state machine language has been inspired by a graphical state machine language RCAT recently developed at the Jet Propulsion Laboratory, as an alternative to using Linear Temporal Logic (LTL) for requirements capture. Transitions between states are labeled with abstract event names and Boolean expressions over such. The abstract events are connected to code fragments using an aspect-oriented pointcut language similar to ASPECTJ's or ASPECTC's pointcut language. The system is implemented in the C analysis and transformation package CIL, and is programmed in OCAML, the implementation language of CIL. The work is closely related to the notion of stateful aspects within aspect-oriented programming, where pointcut languages are extended with temporal assertions over the execution trace.

On Emulation of Flueric Devices in Excitable Chemical Medium

PubMed Central

Adamatzky, Andrew

2016-01-01

Flueric devices are fluidic devices without moving parts. Fluidic devices use fluid as a medium for information transfer and computation. A Belousov-Zhabotinsky (BZ) medium is a thin-layer spatially extended excitable chemical medium which exhibits travelling excitation wave-fronts. The excitation wave-fronts transfer information. Flueric devices compute via jets interaction. BZ devices compute via excitation wave-fronts interaction. In numerical model of BZ medium we show that functions of key flueric devices are implemented in the excitable chemical system: signal generator, and, xor, not and nor Boolean gates, delay elements, diodes and sensors. Flueric devices have been widely used in industry since late 1960s and are still employed in automotive and aircraft technologies. Implementation of analog of the flueric devices in the excitable chemical systems opens doors to further applications of excitation wave-based unconventional computing in soft robotics, embedded organic electronics and living technologies. PMID:27997561

On Emulation of Flueric Devices in Excitable Chemical Medium.

PubMed

Adamatzky, Andrew

2016-01-01

Flueric devices are fluidic devices without moving parts. Fluidic devices use fluid as a medium for information transfer and computation. A Belousov-Zhabotinsky (BZ) medium is a thin-layer spatially extended excitable chemical medium which exhibits travelling excitation wave-fronts. The excitation wave-fronts transfer information. Flueric devices compute via jets interaction. BZ devices compute via excitation wave-fronts interaction. In numerical model of BZ medium we show that functions of key flueric devices are implemented in the excitable chemical system: signal generator, and, xor, not and nor Boolean gates, delay elements, diodes and sensors. Flueric devices have been widely used in industry since late 1960s and are still employed in automotive and aircraft technologies. Implementation of analog of the flueric devices in the excitable chemical systems opens doors to further applications of excitation wave-based unconventional computing in soft robotics, embedded organic electronics and living technologies.

American College of Rheumatology/European League Against Rheumatism remission criteria for rheumatoid arthritis maintain reliable performance when evaluated in 44 joints.

PubMed

Kaneko, Yuko; Kondo, Harumi; Takeuchi, Tsutomu

2013-08-01

To investigate the performance of the new remission criteria for rheumatoid arthritis (RA) in daily clinical practice and the effect of possible misclassification of remission when 44 joints are assessed. Disease activity and remission rate were calculated according to the Disease Activity Score (DAS28), Simplified Disease Activity Index (SDAI), Clinical Disease Activity Index (CDAI), and a Boolean-based definition for 1402 patients with RA in Keio University Hospital. Characteristics of patients in remission were investigated, and the number of misclassified patients was determined--those classified as being in remission based on 28-joint count but as nonremission based on a 44-joint count for each definition criterion. Of all patients analyzed, 46.6%, 45.9%, 41.0%, and 31.5% were classified as in remission in the DAS28, SDAI, CDAI, and Boolean definitions, respectively. Patients classified into remission based only on the DAS28 showed relatively low erythrocyte sedimentation rates but greater swollen joint counts than those classified into remission based on the other definitions. In patients classified into remission based only on the Boolean criteria, the mean physician global assessment was greater than the mean patient global assessment. Although 119 patients had ≤ 1 involved joint in the 28-joint count but > 1 in the 44-joint count, only 34 of these 119 (2.4% of all subjects) were found to have been misclassified into remission. In practice, about half of patients with RA can achieve clinical remission within the DAS28, SDAI, and CDAI; and one-third according to the Boolean-based definition. Patients classified in remission based on a 28-joint count may have pain and swelling in the feet, but misclassification of remission was relatively rare and was seen in only 2.4% of patients under a Boolean definition. The 28-joint count can be sufficient for assessing clinical remission based on the new remission criteria.

Bistatic synthetic aperture radar imaging for arbitrary flight trajectories.

PubMed

Yarman, Can Evren; Yazici, Birsen; Cheney, Margaret

2008-01-01

In this paper, we present an analytic, filtered backprojection (FBP) type inversion method for bistatic synthetic aperture radar (BISAR). We consider a BISAR system where a scene of interest is illuminated by electromagnetic waves that are transmitted, at known times, from positions along an arbitrary, but known, flight trajectory and the scattered waves are measured from positions along a different flight trajectory which is also arbitrary, but known. We assume a single-scattering model for the radar data, and we assume that the ground topography is known but not necessarily flat. We use microlocal analysis to develop the FBP-type reconstruction method. We analyze the computational complexity of the numerical implementation of the method and present numerical simulations to demonstrate its performance.

Efficient cost-sensitive human-machine collaboration for offline signature verification

NASA Astrophysics Data System (ADS)

Coetzer, Johannes; Swanepoel, Jacques; Sabourin, Robert

2012-01-01

We propose a novel strategy for the optimal combination of human and machine decisions in a cost-sensitive environment. The proposed algorithm should be especially beneficial to financial institutions where off-line signatures, each associated with a specific transaction value, require authentication. When presented with a collection of genuine and fraudulent training signatures, produced by so-called guinea pig writers, the proficiency of a workforce of human employees and a score-generating machine can be estimated and represented in receiver operating characteristic (ROC) space. Using a set of Boolean fusion functions, the majority vote decision of the human workforce is combined with each threshold-specific machine-generated decision. The performance of the candidate ensembles is estimated and represented in ROC space, after which only the optimal ensembles and associated decision trees are retained. When presented with a questioned signature linked to an arbitrary writer, the system first uses the ROC-based cost gradient associated with the transaction value to select the ensemble that minimises the expected cost, and then uses the corresponding decision tree to authenticate the signature in question. We show that, when utilising the entire human workforce, the incorporation of a machine streamlines the authentication process and decreases the expected cost for all operating conditions.

Random Boolean networks for autoassociative memory: Optimization and sequential learning

NASA Astrophysics Data System (ADS)

Sherrington, D.; Wong, K. Y. M.

Conventional neural networks are based on synaptic storage of information, even when the neural states are discrete and bounded. In general, the set of potential local operations is much greater. Here we discuss some aspects of the properties of networks of binary neurons with more general Boolean functions controlling the local dynamics. Two specific aspects are emphasised; (i) optimization in the presence of noise and (ii) a simple model for short-term memory exhibiting primacy and recency in the recall of sequentially taught patterns.

Security analysis of boolean algebra based on Zhang-Wang digital signature scheme

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

Zheng, Jinbin, E-mail: jbzheng518@163.com

2014-10-06

In 2005, Zhang and Wang proposed an improvement signature scheme without using one-way hash function and message redundancy. In this paper, we show that this scheme exits potential safety concerns through the analysis of boolean algebra, such as bitwise exclusive-or, and point out that mapping is not one to one between assembly instructions and machine code actually by means of the analysis of the result of the assembly program segment, and which possibly causes safety problems unknown to the software.

Realization of a quantum Hamiltonian Boolean logic gate on the Si(001):H surface.

PubMed

Kolmer, Marek; Zuzak, Rafal; Dridi, Ghassen; Godlewski, Szymon; Joachim, Christian; Szymonski, Marek

2015-08-07

The design and construction of the first prototypical QHC (Quantum Hamiltonian Computing) atomic scale Boolean logic gate is reported using scanning tunnelling microscope (STM) tip-induced atom manipulation on an Si(001):H surface. The NOR/OR gate truth table was confirmed by dI/dU STS (Scanning Tunnelling Spectroscopy) tracking how the surface states of the QHC quantum circuit on the Si(001):H surface are shifted according to the input logical status.

Conference Proceedings on Applied Computational Electromagnetics (3rd) Held in Monterey, California on 24-26 March 1987

DTIC Science & Technology

1987-03-01

the VLSI Implementation of the Electromagnetic Field of an Arbitrary Current Source" B.A. Hoyt, A.J. Terzuoli, A.V. Lair ., Air Force Institute of...method is that cavities of arbitrary three dimensional shapes and nonuniform lossy materials can be analyzed. THEORY OF VECTOR POTENTIAL FINITE...elements used to model the cavity. The method includes the effects of nonuniform lossy materials and can analyze cavities of a wide variety of two- and

A Parallel Vector Machine for the PM Programming Language

NASA Astrophysics Data System (ADS)

Bellerby, Tim

2016-04-01

PM is a new programming language which aims to make the writing of computational geoscience models on parallel hardware accessible to scientists who are not themselves expert parallel programmers. It is based around the concept of communicating operators: language constructs that enable variables local to a single invocation of a parallelised loop to be viewed as if they were arrays spanning the entire loop domain. This mechanism enables different loop invocations (which may or may not be executing on different processors) to exchange information in a manner that extends the successful Communicating Sequential Processes idiom from single messages to collective communication. Communicating operators avoid the additional synchronisation mechanisms, such as atomic variables, required when programming using the Partitioned Global Address Space (PGAS) paradigm. Using a single loop invocation as the fundamental unit of concurrency enables PM to uniformly represent different levels of parallelism from vector operations through shared memory systems to distributed grids. This paper describes an implementation of PM based on a vectorised virtual machine. On a single processor node, concurrent operations are implemented using masked vector operations. Virtual machine instructions operate on vectors of values and may be unmasked, masked using a Boolean field, or masked using an array of active vector cell locations. Conditional structures (such as if-then-else or while statement implementations) calculate and apply masks to the operations they control. A shift in mask representation from Boolean to location-list occurs when active locations become sufficiently sparse. Parallel loops unfold data structures (or vectors of data structures for nested loops) into vectors of values that may additionally be distributed over multiple computational nodes and then split into micro-threads compatible with the size of the local cache. Inter-node communication is accomplished using standard OpenMP and MPI. Performance analyses of the PM vector machine, demonstrating its scaling properties with respect to domain size and the number of processor nodes will be presented for a range of hardware configurations. The PM software and language definition are being made available under unrestrictive MIT and Creative Commons Attribution licenses respectively: www.pm-lang.org.

Saturation: An efficient iteration strategy for symbolic state-space generation

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Luettgen, Gerald; Siminiceanu, Radu; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

This paper presents a novel algorithm for generating state spaces of asynchronous systems using Multi-valued Decision Diagrams. In contrast to related work, the next-state function of a system is not encoded as a single Boolean function, but as cross-products of integer functions. This permits the application of various iteration strategies to build a system's state space. In particular, this paper introduces a new elegant strategy, called saturation, and implements it in the tool SMART. On top of usually performing several orders of magnitude faster than existing BDD-based state-space generators, the algorithm's required peak memory is often close to the nal memory needed for storing the overall state spaces.

Exploring multicriteria decision strategies in GIS with linguistic quantifiers: A case study of residential quality evaluation

NASA Astrophysics Data System (ADS)

Malczewski, Jacek; Rinner, Claus

2005-06-01

Commonly used GIS combination operators such as Boolean conjunction/disjunction and weighted linear combination can be generalized to the ordered weighted averaging (OWA) family of operators. This multicriteria evaluation method allows decision-makers to define a decision strategy on a continuum between pessimistic and optimistic strategies. Recently, OWA has been introduced to GIS-based decision support systems. We propose to extend a previous implementation of OWA with linguistic quantifiers to simplify the definition of decision strategies and to facilitate an exploratory analysis of multiple criteria. The linguistic quantifier-guided OWA procedure is illustrated using a dataset for evaluating residential quality of neighborhoods in London, Ontario.

Complex logic functions implemented with quantum dot bionanophotonic circuits.

PubMed

Claussen, Jonathan C; Hildebrandt, Niko; Susumu, Kimihiro; Ancona, Mario G; Medintz, Igor L

2014-03-26

We combine quantum dots (QDs) with long-lifetime terbium complexes (Tb), a near-IR Alexa Fluor dye (A647), and self-assembling peptides to demonstrate combinatorial and sequential bionanophotonic logic devices that function by time-gated Förster resonance energy transfer (FRET). Upon excitation, the Tb-QD-A647 FRET-complex produces time-dependent photoluminescent signatures from multi-FRET pathways enabled by the capacitor-like behavior of the Tb. The unique photoluminescent signatures are manipulated by ratiometrically varying dye/Tb inputs and collection time. Fluorescent output is converted into Boolean logic states to create complex arithmetic circuits including the half-adder/half-subtractor, 2:1 multiplexer/1:2 demultiplexer, and a 3-digit, 16-combination keypad lock.

Boolean gates on actin filaments

NASA Astrophysics Data System (ADS)

Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew

2016-01-01

Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.

Discrete dynamic modeling of cellular signaling networks.

PubMed

Albert, Réka; Wang, Rui-Sheng

2009-01-01

Understanding signal transduction in cellular systems is a central issue in systems biology. Numerous experiments from different laboratories generate an abundance of individual components and causal interactions mediating environmental and developmental signals. However, for many signal transduction systems there is insufficient information on the overall structure and the molecular mechanisms involved in the signaling network. Moreover, lack of kinetic and temporal information makes it difficult to construct quantitative models of signal transduction pathways. Discrete dynamic modeling, combined with network analysis, provides an effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters. This chapter introduces the fundamental concepts of discrete dynamic modeling, particularly focusing on Boolean dynamic models. We describe this method step-by-step in the context of cellular signaling networks. Several variants of Boolean dynamic models including threshold Boolean networks and piecewise linear systems are also covered, followed by two examples of successful application of discrete dynamic modeling in cell biology.

Origins of Chaos in Autonomous Boolean Networks

NASA Astrophysics Data System (ADS)

Socolar, Joshua; Cavalcante, Hugo; Gauthier, Daniel; Zhang, Rui

2010-03-01

Networks with nodes consisting of ideal Boolean logic gates are known to display either steady states, periodic behavior, or an ultraviolet catastrophe where the number of logic-transition events circulating in the network per unit time grows as a power-law. In an experiment, non-ideal behavior of the logic gates prevents the ultraviolet catastrophe and may lead to deterministic chaos. We identify certain non-ideal features of real logic gates that enable chaos in experimental networks. We find that short-pulse rejection and the asymmetry between the logic states tends to engender periodic behavior. On the other hand, a memory effect termed ``degradation'' can generate chaos. Our results strongly suggest that deterministic chaos can be expected in a large class of experimental Boolean-like networks. Such devices may find application in a variety of technologies requiring fast complex waveforms or flat power spectra. The non-ideal effects identified here also have implications for the statistics of attractors in large complex networks.

Skin Effect Modeling in Conductors of Arbitrary Shape Through a Surface Admittance Operator and the Contour Integral Method

NASA Astrophysics Data System (ADS)

Patel, Utkarsh R.; Triverio, Piero

2016-09-01

An accurate modeling of skin effect inside conductors is of capital importance to solve transmission line and scattering problems. This paper presents a surface-based formulation to model skin effect in conductors of arbitrary cross section, and compute the per-unit-length impedance of a multiconductor transmission line. The proposed formulation is based on the Dirichlet-Neumann operator that relates the longitudinal electric field to the tangential magnetic field on the boundary of a conductor. We demonstrate how the surface operator can be obtained through the contour integral method for conductors of arbitrary shape. The proposed algorithm is simple to implement, efficient, and can handle arbitrary cross-sections, which is a main advantage over the existing approach based on eigenfunctions, which is available only for canonical conductor's shapes. The versatility of the method is illustrated through a diverse set of examples, which includes transmission lines with trapezoidal, curved, and V-shaped conductors. Numerical results demonstrate the accuracy, versatility, and efficiency of the proposed technique.

An efficient matrix-matrix multiplication based antisymmetric tensor contraction engine for general order coupled cluster.

PubMed

Hanrath, Michael; Engels-Putzka, Anna

2010-08-14

In this paper, we present an efficient implementation of general tensor contractions, which is part of a new coupled-cluster program. The tensor contractions, used to evaluate the residuals in each coupled-cluster iteration are particularly important for the performance of the program. We developed a generic procedure, which carries out contractions of two tensors irrespective of their explicit structure. It can handle coupled-cluster-type expressions of arbitrary excitation level. To make the contraction efficient without loosing flexibility, we use a three-step procedure. First, the data contained in the tensors are rearranged into matrices, then a matrix-matrix multiplication is performed, and finally the result is backtransformed to a tensor. The current implementation is significantly more efficient than previous ones capable of treating arbitrary high excitations.

Arbitrary digital pulse sequence generator with delay-loop timing

NASA Astrophysics Data System (ADS)

Hošák, Radim; Ježek, Miroslav

2018-04-01

We propose an idea of an electronic multi-channel arbitrary digital sequence generator with temporal granularity equal to two clock cycles. We implement the generator with 32 channels using a low-cost ARM microcontroller and demonstrate its capability to produce temporal delays ranging from tens of nanoseconds to hundreds of seconds, with 24 ns timing granularity and linear scaling of delay with respect to the number of delay loop iterations. The generator is optionally synchronized with an external clock source to provide 100 ps jitter and overall sequence repeatability within the whole temporal range. The generator is fully programmable and able to produce digital sequences of high complexity. The concept of the generator can be implemented using different microcontrollers and applied for controlling of various optical, atomic, and nuclear physics measurement setups.

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

PubMed Central

Lähdesmäki, Harri; Hautaniemi, Sampsa; Shmulevich, Ilya; Yli-Harja, Olli

2006-01-01

A significant amount of attention has recently been focused on modeling of gene regulatory networks. Two frequently used large-scale modeling frameworks are Bayesian networks (BNs) and Boolean networks, the latter one being a special case of its recent stochastic extension, probabilistic Boolean networks (PBNs). PBN is a promising model class that generalizes the standard rule-based interactions of Boolean networks into the stochastic setting. Dynamic Bayesian networks (DBNs) is a general and versatile model class that is able to represent complex temporal stochastic processes and has also been proposed as a model for gene regulatory systems. In this paper, we concentrate on these two model classes and demonstrate that PBNs and a certain subclass of DBNs can represent the same joint probability distribution over their common variables. The major benefit of introducing the relationships between the models is that it opens up the possibility of applying the standard tools of DBNs to PBNs and vice versa. Hence, the standard learning tools of DBNs can be applied in the context of PBNs, and the inference methods give a natural way of handling the missing values in PBNs which are often present in gene expression measurements. Conversely, the tools for controlling the stationary behavior of the networks, tools for projecting networks onto sub-networks, and efficient learning schemes can be used for DBNs. In other words, the introduced relationships between the models extend the collection of analysis tools for both model classes. PMID:17415411

Quantum Optical Realization of Arbitrary Linear Transformations Allowing for Loss and Gain

NASA Astrophysics Data System (ADS)

Tischler, N.; Rockstuhl, C.; Słowik, K.

2018-04-01

Unitary transformations are routinely modeled and implemented in the field of quantum optics. In contrast, nonunitary transformations, which can involve loss and gain, require a different approach. In this work, we present a universal method to deal with nonunitary networks. An input to the method is an arbitrary linear transformation matrix of optical modes that does not need to adhere to bosonic commutation relations. The method constructs a transformation that includes the network of interest and accounts for full quantum optical effects related to loss and gain. Furthermore, through a decomposition in terms of simple building blocks, it provides a step-by-step implementation recipe, in a manner similar to the decomposition by Reck et al. [Experimental Realization of Any Discrete Unitary Operator, Phys. Rev. Lett. 73, 58 (1994), 10.1103/PhysRevLett.73.58] but applicable to nonunitary transformations. Applications of the method include the implementation of positive-operator-valued measures and the design of probabilistic optical quantum information protocols.

Implementation of Multivariable Logic Functions in Parallel by Electrically Addressing a Molecule of Three Dopants in Silicon.

PubMed

Fresch, Barbara; Bocquel, Juanita; Hiluf, Dawit; Rogge, Sven; Levine, Raphael D; Remacle, Françoise

2017-07-05

To realize low-power, compact logic circuits, one can explore parallel operation on single nanoscale devices. An added incentive is to use multivalued (as distinct from Boolean) logic. Here, we theoretically demonstrate that the computation of all the possible outputs of a multivariate, multivalued logic function can be implemented in parallel by electrical addressing of a molecule made up of three interacting dopant atoms embedded in Si. The electronic states of the dopant molecule are addressed by pulsing a gate voltage. By simulating the time evolution of the non stationary electronic density built by the gate voltage, we show that one can implement a molecular decision tree that provides in parallel all the outputs for all the inputs of the multivariate, multivalued logic function. The outputs are encoded in the populations and in the bond orders of the dopant molecule, which can be measured using an STM tip. We show that the implementation of the molecular logic tree is equivalent to a spectral function decomposition. The function that is evaluated can be field-programmed by changing the time profile of the pulsed gate voltage. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

FRAP and Photoconversion in Multiple Arbitrary Regions of Interest Using a Programmable Array Microscope (PAM)

PubMed Central

Hagen, Guy M.; Caarls, Wouter; Lidke, Keith A.; de Vries, Anthony H. B.; Fritsch, Cornelia; Barisas, B. George; Arndt-Jovin, Donna J.; Jovin, Thomas M.

2011-01-01

Photomanipulation (photobleaching, photoactivation, or photoconversion) is an essential tool in fluorescence microscopy. Fluorescence recovery after photobleaching (FRAP) is commonly used for the determination of lateral diffusion constants of membrane proteins, and can be conveniently implemented in confocal laser scanning microscopy (CLSM). Such determinations provide important information on molecular dynamics in live cells. However, the CLSM platform is inherently limited for FRAP because of its inflexible raster (spot) scanning format. We have implemented FRAP and photoactivation protocols using structured illumination and detection in a programmable array microscope (PAM). The patterns are arbitrary in number and shape, dynamic and adjustable to and by the sample characteristics. We have used multi-spot PAM-FRAP to measure the lateral diffusion of the erbB3 (HER3) receptor tyrosine kinase labeled by fusion with mCitrine on untreated cells and after treatment with reagents that perturb the cytoskeleton or plasma membrane or activate co-expressed erbB1 (HER1, the EGF receptor EGFR). We also show the versatility of the PAM for photoactivation in arbitrary regions of interest, in cells expressing erbB3 fused with the photoconvertible fluorescent protein dronpa. PMID:19208387

Emerald: an object-based language for distributed programming

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

Hutchinson, N.C.

1987-01-01

Distributed systems have become more common, however constructing distributed applications remains a very difficult task. Numerous operating systems and programming languages have been proposed that attempt to simplify the programming of distributed applications. Here a programing language called Emerald is presented that simplifies distributed programming by extending the concepts of object-based languages to the distributed environment. Emerald supports a single model of computation: the object. Emerald objects include private entities such as integers and Booleans, as well as shared, distributed entities such as compilers, directories, and entire file systems. Emerald objects may move between machines in the system, but objectmore » invocation is location independent. The uniform semantic model used for describing all Emerald objects makes the construction of distributed applications in Emerald much simpler than in systems where the differences in implementation between local and remote entities are visible in the language semantics. Emerald incorporates a type system that deals only with the specification of objects - ignoring differences in implementation. Thus, two different implementations of the same abstraction may be freely mixed.« less

Semi-automated contour recognition using DICOMautomaton

NASA Astrophysics Data System (ADS)

Clark, H.; Wu, J.; Moiseenko, V.; Lee, R.; Gill, B.; Duzenli, C.; Thomas, S.

2014-03-01

Purpose: A system has been developed which recognizes and classifies Digital Imaging and Communication in Medicine contour data with minimal human intervention. It allows researchers to overcome obstacles which tax analysis and mining systems, including inconsistent naming conventions and differences in data age or resolution. Methods: Lexicographic and geometric analysis is used for recognition. Well-known lexicographic methods implemented include Levenshtein-Damerau, bag-of-characters, Double Metaphone, Soundex, and (word and character)-N-grams. Geometrical implementations include 3D Fourier Descriptors, probability spheres, boolean overlap, simple feature comparison (e.g. eccentricity, volume) and rule-based techniques. Both analyses implement custom, domain-specific modules (e.g. emphasis differentiating left/right organ variants). Contour labels from 60 head and neck patients are used for cross-validation. Results: Mixed-lexicographical methods show an effective improvement in more than 10% of recognition attempts compared with a pure Levenshtein-Damerau approach when withholding 70% of the lexicon. Domain-specific and geometrical techniques further boost performance. Conclusions: DICOMautomaton allows users to recognize contours semi-automatically. As usage increases and the lexicon is filled with additional structures, performance improves, increasing the overall utility of the system.

Coded diffraction system in X-ray crystallography using a boolean phase coded aperture approximation

NASA Astrophysics Data System (ADS)

Pinilla, Samuel; Poveda, Juan; Arguello, Henry

2018-03-01

Phase retrieval is a problem present in many applications such as optics, astronomical imaging, computational biology and X-ray crystallography. Recent work has shown that the phase can be better recovered when the acquisition architecture includes a coded aperture, which modulates the signal before diffraction, such that the underlying signal is recovered from coded diffraction patterns. Moreover, this type of modulation effect, before the diffraction operation, can be obtained using a phase coded aperture, just after the sample under study. However, a practical implementation of a phase coded aperture in an X-ray application is not feasible, because it is computationally modeled as a matrix with complex entries which requires changing the phase of the diffracted beams. In fact, changing the phase implies finding a material that allows to deviate the direction of an X-ray beam, which can considerably increase the implementation costs. Hence, this paper describes a low cost coded X-ray diffraction system based on block-unblock coded apertures that enables phase reconstruction. The proposed system approximates the phase coded aperture with a block-unblock coded aperture by using the detour-phase method. Moreover, the SAXS/WAXS X-ray crystallography software was used to simulate the diffraction patterns of a real crystal structure called Rhombic Dodecahedron. Additionally, several simulations were carried out to analyze the performance of block-unblock approximations in recovering the phase, using the simulated diffraction patterns. Furthermore, the quality of the reconstructions was measured in terms of the Peak Signal to Noise Ratio (PSNR). Results show that the performance of the block-unblock phase coded apertures approximation decreases at most 12.5% compared with the phase coded apertures. Moreover, the quality of the reconstructions using the boolean approximations is up to 2.5 dB of PSNR less with respect to the phase coded aperture reconstructions.

Symbolic Boolean Manipulation with Ordered Binary Decision Diagrams

DTIC Science & Technology

1992-07-01

memories , where careful attention has been given to programming the memory management routines [Brace et al 19901. To extract maximum performance, it...OBDDs) represent Boolean functions as directed acyclic graphs. They form a canonical representation, making testing of functional properties such as...indicated 3 X X2 X3 f 000 0 0 01 0X22 0 10 0 0 11 1 d 1 0 0 0 X3 X 3X 1 01 1 1 10 0 - i"o11 10o 1 1 Figure 1: Truth Table and Decison Tree Repremmtatios

Generating probabilistic Boolean networks from a prescribed transition probability matrix.

PubMed

Ching, W-K; Chen, X; Tsing, N-K

2009-11-01

Probabilistic Boolean networks (PBNs) have received much attention in modeling genetic regulatory networks. A PBN can be regarded as a Markov chain process and is characterised by a transition probability matrix. In this study, the authors propose efficient algorithms for constructing a PBN when its transition probability matrix is given. The complexities of the algorithms are also analysed. This is an interesting inverse problem in network inference using steady-state data. The problem is important as most microarray data sets are assumed to be obtained from sampling the steady-state.

Consistent Correlations for Parameterised Boolean Equation Systems with Applications in Correctness Proofs for Manipulations

NASA Astrophysics Data System (ADS)

Willemse, Tim A. C.

We introduce the concept of consistent correlations for parameterised Boolean equation systems (PBESs), motivated largely by the laborious proofs of correctness required for most manipulations in this setting. Consistent correlations focus on relating the equations that occur in PBESs, rather than their solutions. For a fragment of PBESs, consistent correlations are shown to coincide with a recently introduced form of bisimulation. Finally, we show that bisimilarity on processes induces consistent correlations on PBESs encoding model checking problems. We apply our theory to two example manipulations from the literature.

A Parallel Approach in Computing Correlation Immunity up to Six Variables

DTIC Science & Technology

2015-03-10

their nonlinearity is divisible by 4. Let CI(n, k) (respectively, BCI (n, k)) be the number of exact order k correlation im- mune, (respectively...further balanced) n-variable Boolean functions. The notations CI(n, k, d), BCI (n, k, d) restricts the previous count to degree d Boolean functions...Theorem 3. The following are true: (i) BCI (n, n, 0) = 0, CI(n, n, 0) = 2, CI(n, k, 1) = BCI (n, k, 1) = 2 ( n k+1 ) , 0 ≤ k ≤ n− 1. (ii) BCI (n, n− 2) = 2

On Weak and Strong 2k- bent Boolean Functions

DTIC Science & Technology

2016-01-01

U.S.A. Email: pstanica@nps.edu Abstract—In this paper we introduce a sequence of discrete Fourier transforms and define new versions of bent...denotes the complex conjugate of z. An important tool in our analysis is the discrete Fourier transform , known in Boolean functions literature, as Walsh...Hadamard, or Walsh–Hadamard transform , which is the func- tion Wf : Fn2 → C, defined by Wf (u) = 2− n 2 ∑ x∈Vn (−1)f(x)⊕u·x. Any f ∈ Bn can be

Qubits and quantum Hamiltonian computing performances for operating a digital Boolean 1/2-adder

NASA Astrophysics Data System (ADS)

Dridi, Ghassen; Faizy Namarvar, Omid; Joachim, Christian

2018-04-01

Quantum Boolean (1 + 1) digits 1/2-adders are designed with 3 qubits for the quantum computing (Qubits) and 4 quantum states for the quantum Hamiltonian computing (QHC) approaches. Detailed analytical solutions are provided to analyse the time operation of those different 1/2-adder gates. QHC is more robust to noise than Qubits and requires about the same amount of energy for running its 1/2-adder logical operations. QHC is faster in time than Qubits but its logical output measurement takes longer.

Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping.

PubMed

Sriram, Ganesh; Shanks, Jacqueline V

2004-04-01

The biosynthetically directed fractional (13)C labeling method for metabolic flux evaluation relies on performing a 2-D [(13)C, (1)H] NMR experiment on extracts from organisms cultured on a uniformly labeled carbon substrate. This article focuses on improvements in the interpretation of data obtained from such an experiment by employing the concept of bondomers. Bondomers take into account the natural abundance of (13)C; therefore many bondomers in a real network are zero, and can be precluded a priori--thus resulting in fewer balances. Using this method, we obtained a set of linear equations which can be solved to obtain analytical formulas for NMR-measurable quantities in terms of fluxes in glycolysis and the pentose phosphate pathways. For a specific case of this network with four degrees of freedom, a priori identifiability of the fluxes was shown possible for any set of fluxes. For a more general case with five degrees of freedom, the fluxes were shown identifiable for a representative set of fluxes. Minimal sets of measurements which best identify the fluxes are listed. Furthermore, we have delineated Boolean function mapping, a new method to iteratively simulate bondomer abundances or efficiently convert carbon skeleton rearrangement information to mapping matrices. The efficiency of this method is expected to be valuable while analyzing metabolic networks which are not completely known (such as in plant metabolism) or while implementing iterative bondomer balancing methods.

Image segmentation by hierarchial agglomeration of polygons using ecological statistics

DOEpatents

Prasad, Lakshman; Swaminarayan, Sriram

2013-04-23

A method for rapid hierarchical image segmentation based on perceptually driven contour completion and scene statistics is disclosed. The method begins with an initial fine-scale segmentation of an image, such as obtained by perceptual completion of partial contours into polygonal regions using region-contour correspondences established by Delaunay triangulation of edge pixels as implemented in VISTA. The resulting polygons are analyzed with respect to their size and color/intensity distributions and the structural properties of their boundaries. Statistical estimates of granularity of size, similarity of color, texture, and saliency of intervening boundaries are computed and formulated into logical (Boolean) predicates. The combined satisfiability of these Boolean predicates by a pair of adjacent polygons at a given segmentation level qualifies them for merging into a larger polygon representing a coarser, larger-scale feature of the pixel image and collectively obtains the next level of polygonal segments in a hierarchy of fine-to-coarse segmentations. The iterative application of this process precipitates textured regions as polygons with highly convolved boundaries and helps distinguish them from objects which typically have more regular boundaries. The method yields a multiscale decomposition of an image into constituent features that enjoy a hierarchical relationship with features at finer and coarser scales. This provides a traversable graph structure from which feature content and context in terms of other features can be derived, aiding in automated image understanding tasks. The method disclosed is highly efficient and can be used to decompose and analyze large images.

Quantitative phase retrieval with arbitrary pupil and illumination

DOE PAGES

Claus, Rene A.; Naulleau, Patrick P.; Neureuther, Andrew R.; ...

2015-10-02

We present a general algorithm for combining measurements taken under various illumination and imaging conditions to quantitatively extract the amplitude and phase of an object wave. The algorithm uses the weak object transfer function, which incorporates arbitrary pupil functions and partially coherent illumination. The approach is extended beyond the weak object regime using an iterative algorithm. Finally, we demonstrate the method on measurements of Extreme Ultraviolet Lithography (EUV) multilayer mask defects taken in an EUV zone plate microscope with both a standard zone plate lens and a zone plate implementing Zernike phase contrast.

Entanglement detection in the vicinity of arbitrary Dicke states.

PubMed

Duan, L-M

2011-10-28

Dicke states represent a class of multipartite entangled states that can be generated experimentally with many applications in quantum information. We propose a method to experimentally detect genuine multipartite entanglement in the vicinity of arbitrary Dicke states. The detection scheme can be used to experimentally quantify the entanglement depth of many-body systems and is easy to implement as it requires measurement of only three collective spin operators. The detection criterion is strong as it heralds multipartite entanglement even in cases where the state fidelity goes down exponentially with the number of qubits.

Quantum Teamwork for Unconditional Multiparty Communication with Gaussian States

NASA Astrophysics Data System (ADS)

Zhang, Jing; Adesso, Gerardo; Xie, Changde; Peng, Kunchi

2009-08-01

We demonstrate the capability of continuous variable Gaussian states to communicate multipartite quantum information. A quantum teamwork protocol is presented according to which an arbitrary possibly entangled multimode state can be faithfully teleported between two teams each comprising many cooperative users. We prove that N-mode Gaussian weighted graph states exist for arbitrary N that enable unconditional quantum teamwork implementations for any arrangement of the teams. These perfect continuous variable maximally multipartite entangled resources are typical among pure Gaussian states and are unaffected by the entanglement frustration occurring in multiqubit states.

Experimental implementation of the Bacon-Shor code with 10 entangled photons

NASA Astrophysics Data System (ADS)

Gimeno-Segovia, Mercedes; Sanders, Barry C.

The number of qubits that can be effectively controlled in quantum experiments is growing, reaching a regime where small quantum error-correcting codes can be tested. The Bacon-Shor code is a simple quantum code that protects against the effect of an arbitrary single-qubit error. In this work, we propose an experimental implementation of said code in a post-selected linear optical setup, similar to the recently reported 10-photon GHZ generation experiment. In the procedure we propose, an arbitrary state is encoded into the protected Shor code subspace, and after undergoing a controlled single-qubit error, is successfully decoded. BCS appreciates financial support from Alberta Innovates, NSERC, China's 1000 Talent Plan and the Institute for Quantum Information and Matter, which is an NSF Physics Frontiers Center(NSF Grant PHY-1125565) with support of the Moore Foundation(GBMF-2644).

Hypergraph partitioning implementation for parallelizing matrix-vector multiplication using CUDA GPU-based parallel computing

NASA Astrophysics Data System (ADS)

Murni, Bustamam, A.; Ernastuti, Handhika, T.; Kerami, D.

2017-07-01

Calculation of the matrix-vector multiplication in the real-world problems often involves large matrix with arbitrary size. Therefore, parallelization is needed to speed up the calculation process that usually takes a long time. Graph partitioning techniques that have been discussed in the previous studies cannot be used to complete the parallelized calculation of matrix-vector multiplication with arbitrary size. This is due to the assumption of graph partitioning techniques that can only solve the square and symmetric matrix. Hypergraph partitioning techniques will overcome the shortcomings of the graph partitioning technique. This paper addresses the efficient parallelization of matrix-vector multiplication through hypergraph partitioning techniques using CUDA GPU-based parallel computing. CUDA (compute unified device architecture) is a parallel computing platform and programming model that was created by NVIDIA and implemented by the GPU (graphics processing unit).

Synchronization Analysis of Master-Slave Probabilistic Boolean Networks.

PubMed

Lu, Jianquan; Zhong, Jie; Li, Lulu; Ho, Daniel W C; Cao, Jinde

2015-08-28

In this paper, we analyze the synchronization problem of master-slave probabilistic Boolean networks (PBNs). The master Boolean network (BN) is a deterministic BN, while the slave BN is determined by a series of possible logical functions with certain probability at each discrete time point. In this paper, we firstly define the synchronization of master-slave PBNs with probability one, and then we investigate synchronization with probability one. By resorting to new approach called semi-tensor product (STP), the master-slave PBNs are expressed in equivalent algebraic forms. Based on the algebraic form, some necessary and sufficient criteria are derived to guarantee synchronization with probability one. Further, we study the synchronization of master-slave PBNs in probability. Synchronization in probability implies that for any initial states, the master BN can be synchronized by the slave BN with certain probability, while synchronization with probability one implies that master BN can be synchronized by the slave BN with probability one. Based on the equivalent algebraic form, some efficient conditions are derived to guarantee synchronization in probability. Finally, several numerical examples are presented to show the effectiveness of the main results.

Verification and Optimal Control of Context-Sensitive Probabilistic Boolean Networks Using Model Checking and Polynomial Optimization

PubMed Central

Hiraishi, Kunihiko

2014-01-01

One of the significant topics in systems biology is to develop control theory of gene regulatory networks (GRNs). In typical control of GRNs, expression of some genes is inhibited (activated) by manipulating external stimuli and expression of other genes. It is expected to apply control theory of GRNs to gene therapy technologies in the future. In this paper, a control method using a Boolean network (BN) is studied. A BN is widely used as a model of GRNs, and gene expression is expressed by a binary value (ON or OFF). In particular, a context-sensitive probabilistic Boolean network (CS-PBN), which is one of the extended models of BNs, is used. For CS-PBNs, the verification problem and the optimal control problem are considered. For the verification problem, a solution method using the probabilistic model checker PRISM is proposed. For the optimal control problem, a solution method using polynomial optimization is proposed. Finally, a numerical example on the WNT5A network, which is related to melanoma, is presented. The proposed methods provide us useful tools in control theory of GRNs. PMID:24587766

Synchronization Analysis of Master-Slave Probabilistic Boolean Networks

PubMed Central

Lu, Jianquan; Zhong, Jie; Li, Lulu; Ho, Daniel W. C.; Cao, Jinde

2015-01-01

In this paper, we analyze the synchronization problem of master-slave probabilistic Boolean networks (PBNs). The master Boolean network (BN) is a deterministic BN, while the slave BN is determined by a series of possible logical functions with certain probability at each discrete time point. In this paper, we firstly define the synchronization of master-slave PBNs with probability one, and then we investigate synchronization with probability one. By resorting to new approach called semi-tensor product (STP), the master-slave PBNs are expressed in equivalent algebraic forms. Based on the algebraic form, some necessary and sufficient criteria are derived to guarantee synchronization with probability one. Further, we study the synchronization of master-slave PBNs in probability. Synchronization in probability implies that for any initial states, the master BN can be synchronized by the slave BN with certain probability, while synchronization with probability one implies that master BN can be synchronized by the slave BN with probability one. Based on the equivalent algebraic form, some efficient conditions are derived to guarantee synchronization in probability. Finally, several numerical examples are presented to show the effectiveness of the main results. PMID:26315380

Magnon-based logic in a multi-terminal YIG/Pt nanostructure

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

Ganzhorn, Kathrin, E-mail: kathrin.ganzhorn@wmi.badw.de; Klingler, Stefan; Wimmer, Tobias

2016-07-11

Boolean logic is the foundation of modern digital information processing. Recently, there has been a growing interest in phenomena based on pure spin currents, which allows to move from charge to spin based logic gates. We study a proof-of-principle logic device based on the ferrimagnetic insulator Yttrium Iron Garnet, with Pt strips acting as injectors and detectors for non-equilibrium magnons. We experimentally observe incoherent superposition of magnons generated by different injectors. This allows to implement a fully functional majority gate, enabling multiple logic operations (AND and OR) in one and the same device. Clocking frequencies of the order of severalmore » GHz and straightforward down-scaling make our device promising for applications.« less

Ad Hoc Information Extraction for Clinical Data Warehouses.

PubMed

Dietrich, Georg; Krebs, Jonathan; Fette, Georg; Ertl, Maximilian; Kaspar, Mathias; Störk, Stefan; Puppe, Frank

2018-05-01

Clinical Data Warehouses (CDW) reuse Electronic health records (EHR) to make their data retrievable for research purposes or patient recruitment for clinical trials. However, much information are hidden in unstructured data like discharge letters. They can be preprocessed and converted to structured data via information extraction (IE), which is unfortunately a laborious task and therefore usually not available for most of the text data in CDW. The goal of our work is to provide an ad hoc IE service that allows users to query text data ad hoc in a manner similar to querying structured data in a CDW. While search engines just return text snippets, our systems also returns frequencies (e.g. how many patients exist with "heart failure" including textual synonyms or how many patients have an LVEF < 45) based on the content of discharge letters or textual reports for special investigations like heart echo. Three subtasks are addressed: (1) To recognize and to exclude negations and their scopes, (2) to extract concepts, i.e. Boolean values and (3) to extract numerical values. We implemented an extended version of the NegEx-algorithm for German texts that detects negations and determines their scope. Furthermore, our document oriented CDW PaDaWaN was extended with query functions, e.g. context sensitive queries and regex queries, and an extraction mode for computing the frequencies for Boolean and numerical values. Evaluations in chest X-ray reports and in discharge letters showed high F1-scores for the three subtasks: Detection of negated concepts in chest X-ray reports with an F1-score of 0.99 and in discharge letters with 0.97; of Boolean values in chest X-ray reports about 0.99, and of numerical values in chest X-ray reports and discharge letters also around 0.99 with the exception of the concept age. The advantages of an ad hoc IE over a standard IE are the low development effort (just entering the concept with its variants), the promptness of the results and the adaptability by the user to his or her particular question. Disadvantage are usually lower accuracy and confidence.This ad hoc information extraction approach is novel and exceeds existing systems: Roogle [1] extracts predefined concepts from texts at preprocessing and makes them retrievable at runtime. Dr. Warehouse [2] applies negation detection and indexes the produced subtexts which include affirmed findings. Our approach combines negation detection and the extraction of concepts. But the extraction does not take place during preprocessing, but at runtime. That provides an ad hoc, dynamic, interactive and adjustable information extraction of random concepts and even their values on the fly at runtime. We developed an ad hoc information extraction query feature for Boolean and numerical values within a CDW with high recall and precision based on a pipeline that detects and removes negations and their scope in clinical texts. Schattauer GmbH.

Automatic numerical evaluation of vacancy-mediated transport for arbitrary crystals: Onsager coefficients in the dilute limit using a Green function approach

NASA Astrophysics Data System (ADS)

Trinkle, Dallas R.

2017-10-01

A general solution for vacancy-mediated diffusion in the dilute-vacancy/dilute-solute limit for arbitrary crystal structures is derived from the master equation. A general numerical approach to the vacancy lattice Green function reduces to the sum of a few analytic functions and numerical integration of a smooth function over the Brillouin zone for arbitrary crystals. The Dyson equation solves for the Green function in the presence of a solute with arbitrary but finite interaction range to compute the transport coefficients accurately, efficiently and automatically, including cases with very large differences in solute-vacancy exchange rates. The methodology takes advantage of the space group symmetry of a crystal to reduce the complexity of the matrix inversion in the Dyson equation. An open-source implementation of the algorithm is available, and numerical results are presented for the convergence of the integration error of the bare vacancy Green function, and tracer correlation factors for a variety of crystals including wurtzite (hexagonal diamond) and garnet.

A survey of SAT solver

NASA Astrophysics Data System (ADS)

Gong, Weiwei; Zhou, Xu

2017-06-01

In Computer Science, the Boolean Satisfiability Problem(SAT) is the problem of determining if there exists an interpretation that satisfies a given Boolean formula. SAT is one of the first problems that was proven to be NP-complete, which is also fundamental to artificial intelligence, algorithm and hardware design. This paper reviews the main algorithms of the SAT solver in recent years, including serial SAT algorithms, parallel SAT algorithms, SAT algorithms based on GPU, and SAT algorithms based on FPGA. The development of SAT is analyzed comprehensively in this paper. Finally, several possible directions for the development of the SAT problem are proposed.

Modeling bidirectional reflectance of forests and woodlands using Boolean models and geometric optics

NASA Technical Reports Server (NTRS)

Strahler, Alan H.; Jupp, David L. B.

1990-01-01

Geometric-optical discrete-element mathematical models for forest canopies have been developed using the Boolean logic and models of Serra. The geometric-optical approach is considered to be particularly well suited to describing the bidirectional reflectance of forest woodland canopies, where the concentration of leaf material within crowns and the resulting between-tree gaps make plane-parallel, radiative-transfer models inappropriate. The approach leads to invertible formulations, in which the spatial and directional variance provides the means for remote estimation of tree crown size, shape, and total cover from remotedly sensed imagery.

A Parallel Approach in Computing Correlation Immunity up to Six Variables

DTIC Science & Technology

2015-07-24

nonlinearity is divisible by 4. Let CI(n, k) (respectively, BCI (n, k)) be the number of exact order k corre- lation immune, (respectively, further...balanced) n-variable Boolean functions. The notations CI(n, k, d), BCI (n, k, d) restricts the previous count to degree d Boolean functions. Theorem 3...The following are true: (i) BCI (n, n, 0) = 0, CI(n, n, 0) = 2, CI(n, k, 1) = BCI (n, k, 1) = 2 ( n k+1 ) , 0 ≤ k ≤ n− 1. (ii) BCI (n, n− 2) = 2 ( n n−1

High speed all optical logic gates based on quantum dot semiconductor optical amplifiers.

PubMed

Ma, Shaozhen; Chen, Zhe; Sun, Hongzhi; Dutta, Niloy K

2010-03-29

A scheme to realize all-optical Boolean logic functions AND, XOR and NOT using semiconductor optical amplifiers with quantum-dot active layers is studied. nonlinear dynamics including carrier heating and spectral hole-burning are taken into account together with the rate equations scheme. Results show with QD excited state and wetting layer serving as dual-reservoir of carriers, as well as the ultra fast carrier relaxation of the QD device, this scheme is suitable for high speed Boolean logic operations. Logic operation can be carried out up to speed of 250 Gb/s.

Arbitrary photonic wave plate operations on chip: Realizing Hadamard, Pauli-X, and rotation gates for polarisation qubits

PubMed Central

Heilmann, René; Gräfe, Markus; Nolte, Stefan; Szameit, Alexander

2014-01-01

Chip-based photonic quantum computing is an emerging technology that promises much speedup over conventional computers at small integration volumes. Particular interest is thereby given to polarisation-encoded photonic qubits, and many protocols have been developed for this encoding. However, arbitrary wave plate operation on chip are not available so far, preventing from the implementation of integrated universal quantum computing algorithms. In our work we close this gap and present Hadamard, Pauli-X, and rotation gates of high fidelity for photonic polarisation qubits on chip by employing a reorientation of the optical axis of birefringent waveguides. The optical axis of the birefringent waveguide is rotated due to the impact of an artificial stress field created by an additional modification close to the waveguide. By adjusting this length of the defect along the waveguide, the retardation between ordinary and extraordinary field components is precisely tunable including half-wave plate and quarter-wave plate operations. Our approach demonstrates the full range control of orientation and strength of the induced birefringence and thus allows arbitrary wave plate operations without affecting the degree of polarisation or introducing additional losses to the waveguides. The implemented gates are tested with classical and quantum light. PMID:24534893

Super learning to hedge against incorrect inference from arbitrary parametric assumptions in marginal structural modeling.

PubMed

Neugebauer, Romain; Fireman, Bruce; Roy, Jason A; Raebel, Marsha A; Nichols, Gregory A; O'Connor, Patrick J

2013-08-01

Clinical trials are unlikely to ever be launched for many comparative effectiveness research (CER) questions. Inferences from hypothetical randomized trials may however be emulated with marginal structural modeling (MSM) using observational data, but success in adjusting for time-dependent confounding and selection bias typically relies on parametric modeling assumptions. If these assumptions are violated, inferences from MSM may be inaccurate. In this article, we motivate the application of a data-adaptive estimation approach called super learning (SL) to avoid reliance on arbitrary parametric assumptions in CER. Using the electronic health records data from adults with new-onset type 2 diabetes, we implemented MSM with inverse probability weighting (IPW) estimation to evaluate the effect of three oral antidiabetic therapies on the worsening of glomerular filtration rate. Inferences from IPW estimation were noticeably sensitive to the parametric assumptions about the associations between both the exposure and censoring processes and the main suspected source of confounding, that is, time-dependent measurements of hemoglobin A1c. SL was successfully implemented to harness flexible confounding and selection bias adjustment from existing machine learning algorithms. Erroneous IPW inference about clinical effectiveness because of arbitrary and incorrect modeling decisions may be avoided with SL. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantum rotation gates with controlled nonadiabatic evolutions

NASA Astrophysics Data System (ADS)

Abdelrahim, Abdelrahman A. H.; Benmachiche, Abderrahim; Subhi Mahmoud, Gharib; Messikh, Azeddine

2018-04-01

Quantum gates can be implemented adiabatically and nonadiabatically. Many schemes used at least two sequentially implemented gates to obtain an arbitrary one-qubit gate. Recently, it has been shown that nonadiabatic gates can be realized by single-shot implementation. It has also been shown that quantum gates can be implemented with controlled adiabatic evolutions. In this paper, we combine the advantage of single-shot implementation with controlled adiabatic evolutions to obtain controlled nonadiabatic evolutions. We also investigate the robustness to different types of errors. We find that the fidelity is close to unity for realistic decoherence rates.

Controlled teleportation with the control of two groups of agents via entanglement

NASA Astrophysics Data System (ADS)

He, Xiao-Ling; Liu, Man; Yang, Chui-Ping

2015-03-01

We present a way for implementing controlled teleportation of an arbitrary unknown pure state of a qutrit with the control of two groups of agents via entanglement. In our proposal, the sender can successfully teleport the qutrit state to a distant receiver with the help of all agents. However, if one agent in each group does not cooperate, the receiver cannot gain any information (including amplitude information or phase information or both) about the qutrit state to be teleported. Since a qubit is a special case of a qutrit when the state lies in a fixed two-dimensional subspace of the qutrit, the present proposal can be also applied in the implementation of controlled teleportation of an arbitrary unknown pure state of a qubit with many control agents in two groups. We note that our proposal is the first one to use two groups of agents to achieve controlled teleportation.

Scheme for implementing perfect quantum teleportation with four-qubit entangled states in cavity quantum electrodynamics

NASA Astrophysics Data System (ADS)

Tang, Jing-Wu; Zhao, Guan-Xiang; He, Xiong-Hui

2011-05-01

Recently, Peng et al. [2010 Eur. Phys. J. D 58 403] proposed to teleport an arbitrary two-qubit state with a family of four-qubit entangled states, which simultaneously include the tensor product of two Bell states, linear cluster state and Dicke-class state. This paper proposes to implement their scheme in cavity quantum electrodynamics and then presents a new family of four-qubit entangled state |Ω4>1234. It simultaneously includes all the well-known four-qubit entangled states which can be used to teleport an arbitrary two-qubit state. The distinct advantage of the scheme is that it only needs a single setup to prepare the whole family of four-qubit entangled states, which will be very convenient for experimental realization. After discussing the experimental condition in detail, we show the scheme may be feasible based on present technology in cavity quantum electrodynamics.

Falcon: automated optimization method for arbitrary assessment criteria

DOEpatents

Yang, Tser-Yuan; Moses, Edward I.; Hartmann-Siantar, Christine

2001-01-01

FALCON is a method for automatic multivariable optimization for arbitrary assessment criteria that can be applied to numerous fields where outcome simulation is combined with optimization and assessment criteria. A specific implementation of FALCON is for automatic radiation therapy treatment planning. In this application, FALCON implements dose calculations into the planning process and optimizes available beam delivery modifier parameters to determine the treatment plan that best meets clinical decision-making criteria. FALCON is described in the context of the optimization of external-beam radiation therapy and intensity modulated radiation therapy (IMRT), but the concepts could also be applied to internal (brachytherapy) radiotherapy. The radiation beams could consist of photons or any charged or uncharged particles. The concept of optimizing source distributions can be applied to complex radiography (e.g. flash x-ray or proton) to improve the imaging capabilities of facilities proposed for science-based stockpile stewardship.

A modal analysis of lamellar diffraction gratings in conical mountings

NASA Technical Reports Server (NTRS)

Li, Lifeng

1992-01-01

A rigorous modal analysis of lamellar grating, i.e., gratings having rectangular grooves, in conical mountings is presented. It is an extension of the analysis of Botten et al. which considered non-conical mountings. A key step in the extension is a decomposition of the electromagnetic field in the grating region into two orthogonal components. A computer program implementing this extended modal analysis is capable of dealing with plane wave diffraction by dielectric and metallic gratings with deep grooves, at arbitrary angles of incidence, and having arbitrary incident polarizations. Some numerical examples are included.

Effect of remission definition on healthcare cost savings estimates for patients with rheumatoid arthritis treated with biologic therapies.

PubMed

Barnabe, Cheryl; Thanh, Nguyen Xuan; Ohinmaa, Arto; Homik, Joanne; Barr, Susan G; Martin, Liam; Maksymowych, Walter P

2014-08-01

Sustained remission in rheumatoid arthritis (RA) results in healthcare utilization cost savings. We evaluated the variation in estimates of savings when different definitions of remission [2011 American College of Rheumatology/European League Against Rheumatism Boolean Definition, Simplified Disease Activity Index (SDAI) ≤ 3.3, Clinical Disease Activity Index (CDAI) ≤ 2.8, and Disease Activity Score-28 (DAS28) ≤ 2.6] are applied. The annual mean healthcare service utilization costs were estimated from provincial physician billing claims, outpatient visits, and hospitalizations, with linkage to clinical data from the Alberta Biologics Pharmacosurveillance Program (ABioPharm). Cost savings in patients who had a 1-year continuous period of remission were compared to those who did not, using 4 definitions of remission. In 1086 patients, sustained remission rates were 16.1% for DAS28, 8.8% for Boolean, 5.5% for CDAI, and 4.2% for SDAI. The estimated mean annual healthcare cost savings per patient achieving remission (relative to not) were SDAI $1928 (95% CI 592, 3264), DAS28 $1676 (95% CI 987, 2365), and Boolean $1259 (95% CI 417, 2100). The annual savings by CDAI remission per patient were not significant at $423 (95% CI -1757, 2602). For patients in DAS28, Boolean, and SDAI remission, savings were seen both in costs directly related to RA and its comorbidities, and in costs for non-RA-related conditions. The magnitude of the healthcare cost savings varies according to the remission definition used in classifying patient disease status. The highest point estimate for cost savings was observed in patients attaining SDAI remission and the least with the CDAI; confidence intervals for these estimates do overlap. Future pharmacoeconomic analyses should employ all response definitions in assessing the influence of treatment.

Modeling and controlling the two-phase dynamics of the p53 network: a Boolean network approach

NASA Astrophysics Data System (ADS)

Lin, Guo-Qiang; Ao, Bin; Chen, Jia-Wei; Wang, Wen-Xu; Di, Zeng-Ru

2014-12-01

Although much empirical evidence has demonstrated that p53 plays a key role in tumor suppression, the dynamics and function of the regulatory network centered on p53 have not yet been fully understood. Here, we develop a Boolean network model to reproduce the two-phase dynamics of the p53 network in response to DNA damage. In particular, we map the fates of cells into two types of Boolean attractors, and we find that the apoptosis attractor does not exist for minor DNA damage, reflecting that the cell is reparable. As the amount of DNA damage increases, the basin of the repair attractor shrinks, accompanied by the rising of the apoptosis attractor and the expansion of its basin, indicating that the cell becomes more irreparable with more DNA damage. For severe DNA damage, the repair attractor vanishes, and the apoptosis attractor dominates the state space, accounting for the exclusive fate of death. Based on the Boolean network model, we explore the significance of links, in terms of the sensitivity of the two-phase dynamics, to perturbing the weights of links and removing them. We find that the links are either critical or ordinary, rather than redundant. This implies that the p53 network is irreducible, but tolerant of small mutations at some ordinary links, and this can be interpreted with evolutionary theory. We further devised practical control schemes for steering the system into the apoptosis attractor in the presence of DNA damage by pinning the state of a single node or perturbing the weight of a single link. Our approach offers insights into understanding and controlling the p53 network, which is of paramount importance for medical treatment and genetic engineering.

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

PubMed Central

Wittmann, Dominik M; Krumsiek, Jan; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Klamt, Steffen; Theis, Fabian J

2009-01-01

Background The understanding of regulatory and signaling networks has long been a core objective in Systems Biology. Knowledge about these networks is mainly of qualitative nature, which allows the construction of Boolean models, where the state of a component is either 'off' or 'on'. While often able to capture the essential behavior of a network, these models can never reproduce detailed time courses of concentration levels. Nowadays however, experiments yield more and more quantitative data. An obvious question therefore is how qualitative models can be used to explain and predict the outcome of these experiments. Results In this contribution we present a canonical way of transforming Boolean into continuous models, where the use of multivariate polynomial interpolation allows transformation of logic operations into a system of ordinary differential equations (ODE). The method is standardized and can readily be applied to large networks. Other, more limited approaches to this task are briefly reviewed and compared. Moreover, we discuss and generalize existing theoretical results on the relation between Boolean and continuous models. As a test case a logical model is transformed into an extensive continuous ODE model describing the activation of T-cells. We discuss how parameters for this model can be determined such that quantitative experimental results are explained and predicted, including time-courses for multiple ligand concentrations and binding affinities of different ligands. This shows that from the continuous model we may obtain biological insights not evident from the discrete one. Conclusion The presented approach will facilitate the interaction between modeling and experiments. Moreover, it provides a straightforward way to apply quantitative analysis methods to qualitatively described systems. PMID:19785753

The DAS28-ESR cutoff value necessary to achieve remission under the new Boolean-based remission criteria in patients receiving tocilizumab.

PubMed

Hirabayashi, Yasuhiko; Ishii, Tomonori

2013-01-01

To seek the cutoff value of the 28-joint disease activity score using erythrocyte sedimentation rate (DAS28-ESR) that is necessary to achieve remission under the new Boolean-based criteria, we analyzed the data for 285 patients with rheumatoid arthritis registered between May 2008 and November 2009 by the Michinoku Tocilizumab Study Group and observed for 1 year after receiving tocilizumab (TCZ) in real clinical practice. Remission rates under the DAS28-ESR criteria and the Boolean criteria were assessed every 6 months after the first TCZ dose. The DAS28-ESR cutoff value necessary to achieve remission under the new criteria was analyzed by receiver operating characteristic (ROC) analysis. Data were analyzed using last observation carried forward. After 12 months of TCZ use, remission was achieved in 164 patients (57.5 %) by DAS28-ESR and 71 patients (24.9 %) under the new criteria for clinical trials. CRP levels scarcely affected remission rates, and the difference between remission rates defined by DAS28-ESR and by the new criteria was mainly due to patient global assessment (PGA). Improvement of PGA was inversely related to disease duration. ROC analysis revealed that the DAS28-ESR cutoff value necessary to predict remission under the new criteria for clinical trials was 1.54, with a sensitivity of 88.7 %, specificity of 85.5 %, positive predictive value of 67.0 %, and negative predictive value of 95.8 %. A DAS28-ESR cutoff value of 1.54 may be reasonable to predict achievement of remission under the new Boolean-based criteria for clinical trials in patients receiving TCZ.

Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion

NASA Astrophysics Data System (ADS)

Olšina, Jan; Kramer, Tobias; Kreisbeck, Christoph; Mančal, Tomáš

2014-10-01

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

Scattering suppression from arbitrary objects in spatially dispersive layered metamaterials

NASA Astrophysics Data System (ADS)

Shalin, Alexander S.; Ginzburg, Pavel; Orlov, Alexey A.; Iorsh, Ivan; Belov, Pavel A.; Kivshar, Yuri S.; Zayats, Anatoly V.

2015-03-01

Concealing objects by making them invisible to an external electromagnetic probe is coined by the term "cloaking." Cloaking devices, having numerous potential applications, are still facing challenges in realization, especially in the visible spectral range. In particular, inherent losses and extreme parameters of metamaterials required for the cloak implementation are the limiting factors. Here, we numerically demonstrate nearly perfect suppression of scattering from arbitrary-shaped objects in spatially dispersive metamaterial acting as an alignment-free concealing cover. We consider a realization of a metamaterial as a metal-dielectric multilayer and demonstrate suppression of scattering from an arbitrary object in forward and backward directions with perfectly preserved wave fronts and less than 10% absolute intensity change, despite spatial dispersion effects present in the composite metamaterial. Beyond the usual scattering suppression applications, the proposed configuration may be used for a simple realization of scattering-free detectors and sensors.

Scheme for Quantum Computing Immune to Decoherence

NASA Technical Reports Server (NTRS)

Williams, Colin; Vatan, Farrokh

2008-01-01

A constructive scheme has been devised to enable mapping of any quantum computation into a spintronic circuit in which the computation is encoded in a basis that is, in principle, immune to quantum decoherence. The scheme is implemented by an algorithm that utilizes multiple physical spins to encode each logical bit in such a way that collective errors affecting all the physical spins do not disturb the logical bit. The scheme is expected to be of use to experimenters working on spintronic implementations of quantum logic. Spintronic computing devices use quantum-mechanical spins (typically, electron spins) to encode logical bits. Bits thus encoded (denoted qubits) are potentially susceptible to errors caused by noise and decoherence. The traditional model of quantum computation is based partly on the assumption that each qubit is implemented by use of a single two-state quantum system, such as an electron or other spin-1.2 particle. It can be surprisingly difficult to achieve certain gate operations . most notably, those of arbitrary 1-qubit gates . in spintronic hardware according to this model. However, ironically, certain 2-qubit interactions (in particular, spin-spin exchange interactions) can be achieved relatively easily in spintronic hardware. Therefore, it would be fortunate if it were possible to implement any 1-qubit gate by use of a spin-spin exchange interaction. While such a direct representation is not possible, it is possible to achieve an arbitrary 1-qubit gate indirectly by means of a sequence of four spin-spin exchange interactions, which could be implemented by use of four exchange gates. Accordingly, the present scheme provides for mapping any 1-qubit gate in the logical basis into an equivalent sequence of at most four spin-spin exchange interactions in the physical (encoded) basis. The complexity of the mathematical derivation of the scheme from basic quantum principles precludes a description within this article; it must suffice to report that the derivation provides explicit constructions for finding the exchange couplings in the physical basis needed to implement any arbitrary 1-qubit gate. These constructions lead to spintronic encodings of quantum logic that are more efficient than those of a previously published scheme that utilizes a universal but fixed set of gates.

Stand-alone front-end system for high- frequency, high-frame-rate coded excitation ultrasonic imaging.

PubMed

Park, Jinhyoung; Hu, Changhong; Shung, K Kirk

2011-12-01

A stand-alone front-end system for high-frequency coded excitation imaging was implemented to achieve a wider dynamic range. The system included an arbitrary waveform amplifier, an arbitrary waveform generator, an analog receiver, a motor position interpreter, a motor controller and power supplies. The digitized arbitrary waveforms at a sampling rate of 150 MHz could be programmed and converted to an analog signal. The pulse was subsequently amplified to excite an ultrasound transducer, and the maximum output voltage level achieved was 120 V(pp). The bandwidth of the arbitrary waveform amplifier was from 1 to 70 MHz. The noise figure of the preamplifier was less than 7.7 dB and the bandwidth was 95 MHz. Phantoms and biological tissues were imaged at a frame rate as high as 68 frames per second (fps) to evaluate the performance of the system. During the measurement, 40-MHz lithium niobate (LiNbO(3)) single-element lightweight (<;0.28 g) transducers were utilized. The wire target measure- ment showed that the -6-dB axial resolution of a chirp-coded excitation was 50 μm and lateral resolution was 120 μm. The echo signal-to-noise ratios were found to be 54 and 65 dB for the short burst and coded excitation, respectively. The contrast resolution in a sphere phantom study was estimated to be 24 dB for the chirp-coded excitation and 15 dB for the short burst modes. In an in vivo study, zebrafish and mouse hearts were imaged. Boundaries of the zebrafish heart in the image could be differentiated because of the low-noise operation of the implemented system. In mouse heart images, valves and chambers could be readily visualized with the coded excitation.

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

Miyadera, Takayuki; Imai, Hideki; Graduate School of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551

This paper discusses the no-cloning theorem in a logicoalgebraic approach. In this approach, an orthoalgebra is considered as a general structure for propositions in a physical theory. We proved that an orthoalgebra admits cloning operation if and only if it is a Boolean algebra. That is, only classical theory admits the cloning of states. If unsharp propositions are to be included in the theory, then a notion of effect algebra is considered. We proved that an atomic Archimedean effect algebra admitting cloning operation is a Boolean algebra. This paper also presents a partial result, indicating a relation between the cloningmore » on effect algebras and hidden variables.« less

Diagnostic reasoning techniques for selective monitoring

NASA Technical Reports Server (NTRS)

Homem-De-mello, L. S.; Doyle, R. J.

1991-01-01

An architecture for using diagnostic reasoning techniques in selective monitoring is presented. Given the sensor readings and a model of the physical system, a number of assertions are generated and expressed as Boolean equations. The resulting system of Boolean equations is solved symbolically. Using a priori probabilities of component failure and Bayes' rule, revised probabilities of failure can be computed. These will indicate what components have failed or are the most likely to have failed. This approach is suitable for systems that are well understood and for which the correctness of the assertions can be guaranteed. Also, the system must be such that changes are slow enough to allow the computation.

Computer Program Development Specification for Ada Integrated Environment. Ada Compiler Phases B5-AIE (1). COMP (1).

DTIC Science & Technology

1982-11-05

routines required by the Back End. 3.3 Detailed Functional Requirements 3.3.1 Front End 3.3.1.1 DRIVER The DRIVER is the primary user interface to the...Main 2. Exam ple" !.i ,, , ,vari able • id -: go for B Boolean Ai ’ A" ’ I type d 1 I , for Boolean I (from Standard) i I - - for A function i fuction ...TN in. If a TN cannot be allocated to the primary area of storage it needs(such as a register) it is allocated to the spill area reserved in the local

Concept locator: a client-server application for retrieval of UMLS metathesaurus concepts through complex boolean query.

PubMed

Nadkarni, P M

1997-08-01

Concept Locator (CL) is a client-server application that accesses a Sybase relational database server containing a subset of the UMLS Metathesaurus for the purpose of retrieval of concepts corresponding to one or more query expressions supplied to it. CL's query grammar permits complex Boolean expressions, wildcard patterns, and parenthesized (nested) subexpressions. CL translates the query expressions supplied to it into one or more SQL statements that actually perform the retrieval. The generated SQL is optimized by the client to take advantage of the strengths of the server's query optimizer, and sidesteps its weaknesses, so that execution is reasonably efficient.

A comparison of Boolean-based retrieval to the WAIS system for retrieval of aeronautical information

NASA Technical Reports Server (NTRS)

Marchionini, Gary; Barlow, Diane

1994-01-01

An evaluation of an information retrieval system using a Boolean-based retrieval engine and inverted file architecture and WAIS, which uses a vector-based engine, was conducted. Four research questions in aeronautical engineering were used to retrieve sets of citations from the NASA Aerospace Database which was mounted on a WAIS server and available through Dialog File 108 which served as the Boolean-based system (BBS). High recall and high precision searches were done in the BBS and terse and verbose queries were used in the WAIS condition. Precision values for the WAIS searches were consistently above the precision values for high recall BBS searches and consistently below the precision values for high precision BBS searches. Terse WAIS queries gave somewhat better precision performance than verbose WAIS queries. In every case, a small number of relevant documents retrieved by one system were not retrieved by the other, indicating the incomplete nature of the results from either retrieval system. Relevant documents in the WAIS searches were found to be randomly distributed in the retrieved sets rather than distributed by ranks. Advantages and limitations of both types of systems are discussed.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure

NASA Astrophysics Data System (ADS)

Ciandrini, L.; Maffi, C.; Motta, A.; Bassetti, B.; Cosentino Lagomarsino, M.

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter γ . We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying γ , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks

NASA Astrophysics Data System (ADS)

Villegas, Pablo; Ruiz-Franco, José; Hidalgo, Jorge; Muñoz, Miguel A.

2016-10-01

Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline between their ordered and disordered phases. Critical networks have been argued to lead to a number of functional advantages such as maximal dynamical range, maximal sensitivity to environmental changes, as well as to an excellent tradeoff between stability and flexibility. Here, we study the effect of noise within the context of Boolean networks trained to learn complex tasks under supervision. We verify that quasi-critical networks are the ones learning in the fastest possible way -even for asynchronous updating rules- and that the larger the task complexity the smaller the distance to criticality. On the other hand, when additional sources of intrinsic noise in the network states and/or in its wiring pattern are introduced, the optimally performing networks become clearly subcritical. These results suggest that in order to compensate for inherent stochasticity, regulatory and other type of biological networks might become subcritical rather than being critical, all the most if the task to be performed has limited complexity.

On the number of different dynamics in Boolean networks with deterministic update schedules.

PubMed

Aracena, J; Demongeot, J; Fanchon, E; Montalva, M

2013-04-01

Deterministic Boolean networks are a type of discrete dynamical systems widely used in the modeling of genetic networks. The dynamics of such systems is characterized by the local activation functions and the update schedule, i.e., the order in which the nodes are updated. In this paper, we address the problem of knowing the different dynamics of a Boolean network when the update schedule is changed. We begin by proving that the problem of the existence of a pair of update schedules with different dynamics is NP-complete. However, we show that certain structural properties of the interaction diagraph are sufficient for guaranteeing distinct dynamics of a network. In [1] the authors define equivalence classes which have the property that all the update schedules of a given class yield the same dynamics. In order to determine the dynamics associated to a network, we develop an algorithm to efficiently enumerate the above equivalence classes by selecting a representative update schedule for each class with a minimum number of blocks. Finally, we run this algorithm on the well known Arabidopsis thaliana network to determine the full spectrum of its different dynamics. Copyright © 2013 Elsevier Inc. All rights reserved.

Feedback topology and XOR-dynamics in Boolean networks with varying input structure.

PubMed

Ciandrini, L; Maffi, C; Motta, A; Bassetti, B; Cosentino Lagomarsino, M

2009-08-01

We analyze a model of fixed in-degree random Boolean networks in which the fraction of input-receiving nodes is controlled by the parameter gamma. We investigate analytically and numerically the dynamics of graphs under a parallel XOR updating scheme. This scheme is interesting because it is accessible analytically and its phenomenology is at the same time under control and as rich as the one of general Boolean networks. We give analytical formulas for the dynamics on general graphs, showing that with a XOR-type evolution rule, dynamic features are direct consequences of the topological feedback structure, in analogy with the role of relevant components in Kauffman networks. Considering graphs with fixed in-degree, we characterize analytically and numerically the feedback regions using graph decimation algorithms (Leaf Removal). With varying gamma , this graph ensemble shows a phase transition that separates a treelike graph region from one in which feedback components emerge. Networks near the transition point have feedback components made of disjoint loops, in which each node has exactly one incoming and one outgoing link. Using this fact, we provide analytical estimates of the maximum period starting from topological considerations.

Boolean logic analysis for flow regime recognition of gas-liquid horizontal flow

NASA Astrophysics Data System (ADS)

Ramskill, Nicholas P.; Wang, Mi

2011-10-01

In order to develop a flowmeter for the accurate measurement of multiphase flows, it is of the utmost importance to correctly identify the flow regime present to enable the selection of the optimal method for metering. In this study, the horizontal flow of air and water in a pipeline was studied under a multitude of conditions using electrical resistance tomography but the flow regimes that are presented in this paper have been limited to plug and bubble air-water flows. This study proposes a novel method for recognition of the prevalent flow regime using only a fraction of the data, thus rendering the analysis more efficient. By considering the average conductivity of five zones along the central axis of the tomogram, key features can be identified, thus enabling the recognition of the prevalent flow regime. Boolean logic and frequency spectrum analysis has been applied for flow regime recognition. Visualization of the flow using the reconstructed images provides a qualitative comparison between different flow regimes. Application of the Boolean logic scheme enables a quantitative comparison of the flow patterns, thus reducing the subjectivity in the identification of the prevalent flow regime.

Graph theory approach to the eigenvalue problem of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.; Bainum, P. M.

1981-01-01

Graph theory is used to obtain numerical solutions to eigenvalue problems of large space structures (LSS) characterized by a state vector of large dimensions. The LSS are considered as large, flexible systems requiring both orientation and surface shape control. Graphic interpretation of the determinant of a matrix is employed to reduce a higher dimensional matrix into combinations of smaller dimensional sub-matrices. The reduction is implemented by means of a Boolean equivalent of the original matrices formulated to obtain smaller dimensional equivalents of the original numerical matrix. Computation time becomes less and more accurate solutions are possible. An example is provided in the form of a free-free square plate. Linearized system equations and numerical values of a stiffness matrix are presented, featuring a state vector with 16 components.

Arbitrary waveform modulated pulse EPR at 200 GHz

NASA Astrophysics Data System (ADS)

Kaminker, Ilia; Barnes, Ryan; Han, Songi

2017-06-01

We report here on the implementation of arbitrary waveform generation (AWG) capabilities at ∼200 GHz into an Electron Paramagnetic Resonance (EPR) and Dynamic Nuclear Polarization (DNP) instrument platform operating at 7 T. This is achieved with the integration of a 1 GHz, 2 channel, digital to analog converter (DAC) board that enables the generation of coherent arbitrary waveforms at Ku-band frequencies with 1 ns resolution into an existing architecture of a solid state amplifier multiplier chain (AMC). This allows for the generation of arbitrary phase- and amplitude-modulated waveforms at 200 GHz with >150 mW power. We find that the non-linearity of the AMC poses significant difficulties in generating amplitude-modulated pulses at 200 GHz. We demonstrate that in the power-limited regime of ω1 < 1 MHz phase-modulated pulses were sufficient to achieve significant improvements in broadband (>10 MHz) spin manipulation in incoherent (inversion), as well as coherent (echo formation) experiments. Highlights include the improvement by one order of magnitude in inversion bandwidth compared to that of conventional rectangular pulses, as well as a factor of two in improvement in the refocused echo intensity at 200 GHz.

Probabilistic Teleportation of an Arbitrary Two-Qubit State via Positive Operator-Valued Measurement with Multi Parties

NASA Astrophysics Data System (ADS)

Shi, Lei; Wei, Jia-Hua; Li, Yun-Xia; Ma, Li-Hua; Xue, Yang; Luo, Jun-Wen

2017-04-01

We propose a novel scheme to probabilistically transmit an arbitrary unknown two-qubit quantum state via Positive Operator-Valued Measurement with the help of two partially entangled states. In this scheme, the teleportation with two senders and two receives can be realized when the information of non-maximally entangled states is only available for the senders. Furthermore, the concrete implementation processes of this proposal are presented, meanwhile the classical communication cost and the successful probability of our scheme are calculated. Supported by the National Natural Science Foundation of China under Grant Nos. 60974037, 61134008, 11074307, and 61273202

Polarization-multiplexed plasmonic phase generation with distributed nanoslits.

PubMed

Lee, Seung-Yeol; Kim, Kyuho; Lee, Gun-Yeal; Lee, Byoungho

2015-06-15

Methods for multiplexing surface plasmon polaritons (SPPs) have been attracting much attention due to their potentials for plasmonic integrated systems, plasmonic holography, and optical tweezing. Here, using closely-distanced distributed nanoslits, we propose a method for generating polarization-multiplexed SPP phase profiles which can be applied for implementing general SPP phase distributions. Two independent types of SPP phase generation mechanisms - polarization-independent and polarization-reversible ones - are combined to generate fully arbitrary phase profiles for each optical handedness. As a simple verification of the proposed scheme, we experimentally demonstrate that the location of plasmonic focus can be arbitrary designed, and switched by the change of optical handedness.

Adding control to arbitrary unknown quantum operations

PubMed Central

Zhou, Xiao-Qi; Ralph, Timothy C.; Kalasuwan, Pruet; Zhang, Mian; Peruzzo, Alberto; Lanyon, Benjamin P.; O'Brien, Jeremy L.

2011-01-01

Although quantum computers promise significant advantages, the complexity of quantum algorithms remains a major technological obstacle. We have developed and demonstrated an architecture-independent technique that simplifies adding control qubits to arbitrary quantum operations—a requirement in many quantum algorithms, simulations and metrology. The technique, which is independent of how the operation is done, does not require knowledge of what the operation is, and largely separates the problems of how to implement a quantum operation in the laboratory and how to add a control. Here, we demonstrate an entanglement-based version in a photonic system, realizing a range of different two-qubit gates with high fidelity. PMID:21811242

Generation of five phase-locked harmonics in the continuous wave regime and its potential application to arbitrary optical waveform synthesis

NASA Astrophysics Data System (ADS)

Suhaimi, N. Sheeda; Ohae, C.; Gavara, T.; Nakagawa, K.; Hong, F.-L.; Katsuragawa, M.

2017-08-01

We have successfully generated a new broadband coherent light source in the continuous wave (CW) regime which is an ensemble of multi-harmonic radiations (2403, 1201, 801, 600 and 480 nm) by implementing a frequency dividing technology. The system is uniquely designed that all the harmonics are generated and propagate coaxially which gives the advantage of robustly maintaining the phase coherence among the harmonics. The highlight is its huge potential for the arbitrary optical waveform synthesis in the CW regime which has not been performed yet due to the limitation of the existing light source.

General implementation of arbitrary nonlinear quadrature phase gates

NASA Astrophysics Data System (ADS)

Marek, Petr; Filip, Radim; Ogawa, Hisashi; Sakaguchi, Atsushi; Takeda, Shuntaro; Yoshikawa, Jun-ichi; Furusawa, Akira

2018-02-01

We propose general methodology of deterministic single-mode quantum interaction nonlinearly modifying single quadrature variable of a continuous-variable system. The methodology is based on linear coupling of the system to ancillary systems subsequently measured by quadrature detectors. The nonlinear interaction is obtained by using the data from the quadrature detection for dynamical manipulation of the coupling parameters. This measurement-induced methodology enables direct realization of arbitrary nonlinear quadrature interactions without the need to construct them from the lowest-order gates. Such nonlinear interactions are crucial for more practical and efficient manipulation of continuous quadrature variables as well as qubits encoded in continuous-variable systems.

Quantum mechanics in noninertial reference frames: Relativistic accelerations and fictitious forces

NASA Astrophysics Data System (ADS)

Klink, W. H.; Wickramasekara, S.

2016-06-01

One-particle systems in relativistically accelerating reference frames can be associated with a class of unitary representations of the group of arbitrary coordinate transformations, an extension of the Wigner-Bargmann definition of particles as the physical realization of unitary irreducible representations of the Poincaré group. Representations of the group of arbitrary coordinate transformations become necessary to define unitary operators implementing relativistic acceleration transformations in quantum theory because, unlike in the Galilean case, the relativistic acceleration transformations do not themselves form a group. The momentum operators that follow from these representations show how the fictitious forces in noninertial reference frames are generated in quantum theory.

Binary full adder, made of fusion gates, in a subexcitable Belousov-Zhabotinsky system

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2015-09-01

In an excitable thin-layer Belousov-Zhabotinsky (BZ) medium a localized perturbation leads to the formation of omnidirectional target or spiral waves of excitation. A subexcitable BZ medium responds to asymmetric local perturbation by producing traveling localized excitation wave-fragments, distant relatives of dissipative solitons. The size and life span of an excitation wave-fragment depend on the illumination level of the medium. Under the right conditions the wave-fragments conserve their shape and velocity vectors for extended time periods. I interpret the wave-fragments as values of Boolean variables. When two or more wave-fragments collide they annihilate or merge into a new wave-fragment. States of the logic variables, represented by the wave-fragments, are changed in the result of the collision between the wave-fragments. Thus, a logical gate is implemented. Several theoretical designs and experimental laboratory implementations of Boolean logic gates have been proposed in the past but little has been done cascading the gates into binary arithmetical circuits. I propose a unique design of a binary one-bit full adder based on a fusion gate. A fusion gate is a two-input three-output logical device which calculates the conjunction of the input variables and the conjunction of one input variable with the negation of another input variable. The gate is made of three channels: two channels cross each other at an angle, a third channel starts at the junction. The channels contain a BZ medium. When two excitation wave-fragments, traveling towards each other along input channels, collide at the junction they merge into a single wave-front traveling along the third channel. If there is just one wave-front in the input channel, the front continues its propagation undisturbed. I make a one-bit full adder by cascading two fusion gates. I show how to cascade the adder blocks into a many-bit full adder. I evaluate the feasibility of my designs by simulating the evolution of excitation in the gates and adders using the numerical integration of Oregonator equations.

Boolean function applied to Mimosa pudica movements.

PubMed

De Luccia, Thiago Paes de Barros; Friedman, Pedro

2011-09-01

Seismonastic or thigmonastic movements of Mimosa pudica L. is mostly because of the fast loss of water from swollen motor cells, resulting in temporary collapse of cells and quick curvature in the parts where these cells are located. Because of this, the plant has been much studied since the 18th century, leading us to think about the classical binomial stimulus-response (action-reaction) when compared to animals. Mechanic and electrical stimuli were used to investigate the analogy of mimosa branch with an artificial neuron model and to observe the action potential propagation through the mimosa branch. Boolean function applied to the mimosa branch in analogy with an artificial neuron model is one of the peculiarities of our hypothesis.

Reservoir computing with a single time-delay autonomous Boolean node

NASA Astrophysics Data System (ADS)

Haynes, Nicholas D.; Soriano, Miguel C.; Rosin, David P.; Fischer, Ingo; Gauthier, Daniel J.

2015-02-01

We demonstrate reservoir computing with a physical system using a single autonomous Boolean logic element with time-delay feedback. The system generates a chaotic transient with a window of consistency lasting between 30 and 300 ns, which we show is sufficient for reservoir computing. We then characterize the dependence of computational performance on system parameters to find the best operating point of the reservoir. When the best parameters are chosen, the reservoir is able to classify short input patterns with performance that decreases over time. In particular, we show that four distinct input patterns can be classified for 70 ns, even though the inputs are only provided to the reservoir for 7.5 ns.

Questions Revisited: A Close Examination of Calculus of Inference and Inquiry

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.; Koga, Dennis (Technical Monitor)

2003-01-01

In this paper I examine more closely the way in which probability theory, the calculus of inference, is derived from the Boolean lattice structure of logical assertions ordered by implication. I demonstrate how the duality between the logical conjunction and disjunction in Boolean algebra is lost when deriving the probability calculus. In addition, I look more closely at the other lattice identities to verify that they are satisfied by the probability calculus. Last, I look towards developing the calculus of inquiry demonstrating that there is a sum and product rule for the relevance measure as well as a Bayes theorem. Current difficulties in deriving the complete inquiry calculus will also be discussed.

Optical reversible programmable Boolean logic unit.

PubMed

Chattopadhyay, Tanay

2012-07-20

Computing with reversibility is the only way to avoid dissipation of energy associated with bit erase. So, a reversible microprocessor is required for future computing. In this paper, a design of a simple all-optical reversible programmable processor is proposed using a polarizing beam splitter, liquid crystal-phase spatial light modulators, a half-wave plate, and plane mirrors. This circuit can perform 16 logical operations according to three programming inputs. Also, inputs can be easily recovered from the outputs. It is named the "reversible programmable Boolean logic unit (RPBLU)." The logic unit is the basic building block of many complex computational operations. Hence the design is important in sense. Two orthogonally polarized lights are defined here as two logical states, respectively.

Extending Clause Learning of SAT Solvers with Boolean Gröbner Bases

NASA Astrophysics Data System (ADS)

Zengler, Christoph; Küchlin, Wolfgang

We extend clause learning as performed by most modern SAT Solvers by integrating the computation of Boolean Gröbner bases into the conflict learning process. Instead of learning only one clause per conflict, we compute and learn additional binary clauses from a Gröbner basis of the current conflict. We used the Gröbner basis engine of the logic package Redlog contained in the computer algebra system Reduce to extend the SAT solver MiniSAT with Gröbner basis learning. Our approach shows a significant reduction of conflicts and a reduction of restarts and computation time on many hard problems from the SAT 2009 competition.

Adaptation and survivors in a random Boolean network.

PubMed

Nakamura, Ikuo

2002-04-01

We introduce the competitive agent with imitation strategy in a random Boolean network, in which the agent plays a competitive game that rewards those in minority. After a long time interval, the worst performer changes its strategy to the one of the best and the process is repeated. The network, initially in a chaotic state, evolves to an intermittent state and finally reaches a frozen state. Time series of survived species (whose strategies are imitated by other agents) in the system depend on the connectivity of each agent. In a system with various connectivity groups, the low connectivity groups win the minority game over the high connectivity groups. We also compared the result with mutation strategy system.

Electrooptical adaptive switching network for the hypercube computer

NASA Technical Reports Server (NTRS)

Chow, E.; Peterson, J.

1988-01-01

An all-optical network design for the hyperswitch network using regular free-space interconnects between electronic processor nodes is presented. The adaptive routing model used is described, and an adaptive routing control example is presented. The design demonstrates that existing electrooptical techniques are sufficient for implementing efficient parallel architectures without the need for more complex means of implementing arbitrary interconnection schemes. The electrooptical hyperswitch network significantly improves the communication performance of the hypercube computer.

Fault-tolerant composite Householder reflection

NASA Astrophysics Data System (ADS)

Torosov, Boyan T.; Kyoseva, Elica; Vitanov, Nikolay V.

2015-07-01

We propose a fault-tolerant implementation of the quantum Householder reflection, which is a key operation in various quantum algorithms, quantum-state engineering, generation of arbitrary unitaries, and entanglement characterization. We construct this operation using the modular approach of composite pulses and a relation between the Householder reflection and the quantum phase gate. The proposed implementation is highly insensitive to variations in the experimental parameters, which makes it suitable for high-fidelity quantum information processing.

An implemented method of asymmetric transmission for arbitrary polarization base in multi-layered chiral meta-surface

NASA Astrophysics Data System (ADS)

Xiao, Zhong-yin; Zou, Huan-ling; Xu, Kai-Kai; Tang, Jing-yao

2018-03-01

Asymmetric transmission of linearly or circularly polarized waves is a well-established property not only for three-layered chiral structures but for multi-layered ones. Here we show a method which can simultaneously implement asymmetric transmission for arbitrary base vector polarized wave in multi-layered chiral meta-surface. We systematically study the implemented method based on a multi-layered chiral structure consisting of a y-shape, a half gammadion and an S-shape in the terahertz gap. A numerical simulation was carried out, followed by an explanation of the asymmetric transmission mechanism in these structures proposed in this work. The simulated results indicate that the multi-layered chiral structure can realize a maximum asymmetric transmission of 0.89 and 0.28 for circularly and linearly polarized waves, respectively, which exhibit magnitude improvement over previous chiral metamaterials. Specifically, the maximum asymmetric transmitted coefficient of the multi-layered chiral structure is insensitivity to the incident angles from 0° to 45° for circularly polarized components. Additionally, we also study the influence of structural parameters on the asymmetric transmission effect for both linearly and circularly polarized waves in detail.

Solving Nonlinear Euler Equations with Arbitrary Accuracy

NASA Technical Reports Server (NTRS)

Dyson, Rodger W.

2005-01-01

A computer program that efficiently solves the time-dependent, nonlinear Euler equations in two dimensions to an arbitrarily high order of accuracy has been developed. The program implements a modified form of a prior arbitrary- accuracy simulation algorithm that is a member of the class of algorithms known in the art as modified expansion solution approximation (MESA) schemes. Whereas millions of lines of code were needed to implement the prior MESA algorithm, it is possible to implement the present MESA algorithm by use of one or a few pages of Fortran code, the exact amount depending on the specific application. The ability to solve the Euler equations to arbitrarily high accuracy is especially beneficial in simulations of aeroacoustic effects in settings in which fully nonlinear behavior is expected - for example, at stagnation points of fan blades, where linearizing assumptions break down. At these locations, it is necessary to solve the full nonlinear Euler equations, and inasmuch as the acoustical energy is of the order of 4 to 5 orders of magnitude below that of the mean flow, it is necessary to achieve an overall fractional error of less than 10-6 in order to faithfully simulate entropy, vortical, and acoustical waves.

Rigorously modeling self-stabilizing fault-tolerant circuits: An ultra-robust clocking scheme for systems-on-chip.

PubMed

Dolev, Danny; Függer, Matthias; Posch, Markus; Schmid, Ulrich; Steininger, Andreas; Lenzen, Christoph

2014-06-01

We present the first implementation of a distributed clock generation scheme for Systems-on-Chip that recovers from an unbounded number of arbitrary transient faults despite a large number of arbitrary permanent faults. We devise self-stabilizing hardware building blocks and a hybrid synchronous/asynchronous state machine enabling metastability-free transitions of the algorithm's states. We provide a comprehensive modeling approach that permits to prove, given correctness of the constructed low-level building blocks, the high-level properties of the synchronization algorithm (which have been established in a more abstract model). We believe this approach to be of interest in its own right, since this is the first technique permitting to mathematically verify, at manageable complexity, high-level properties of a fault-prone system in terms of its very basic components. We evaluate a prototype implementation, which has been designed in VHDL, using the Petrify tool in conjunction with some extensions, and synthesized for an Altera Cyclone FPGA.

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

PubMed

Diaz-Uriarte, Ramon

2017-06-15

OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. ramon.diaz@iib.uam.es. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Rigorously modeling self-stabilizing fault-tolerant circuits: An ultra-robust clocking scheme for systems-on-chip☆

PubMed Central

Dolev, Danny; Függer, Matthias; Posch, Markus; Schmid, Ulrich; Steininger, Andreas; Lenzen, Christoph

2014-01-01

We present the first implementation of a distributed clock generation scheme for Systems-on-Chip that recovers from an unbounded number of arbitrary transient faults despite a large number of arbitrary permanent faults. We devise self-stabilizing hardware building blocks and a hybrid synchronous/asynchronous state machine enabling metastability-free transitions of the algorithm's states. We provide a comprehensive modeling approach that permits to prove, given correctness of the constructed low-level building blocks, the high-level properties of the synchronization algorithm (which have been established in a more abstract model). We believe this approach to be of interest in its own right, since this is the first technique permitting to mathematically verify, at manageable complexity, high-level properties of a fault-prone system in terms of its very basic components. We evaluate a prototype implementation, which has been designed in VHDL, using the Petrify tool in conjunction with some extensions, and synthesized for an Altera Cyclone FPGA. PMID:26516290

Efficient eigenvalue determination for arbitrary Pauli products based on generalized spin-spin interactions

NASA Astrophysics Data System (ADS)

Leibfried, D.; Wineland, D. J.

2018-03-01

Effective spin-spin interactions between ? qubits enable the determination of the eigenvalue of an arbitrary Pauli product of dimension N with a constant, small number of multi-qubit gates that is independent of N and encodes the eigenvalue in the measurement basis states of an extra ancilla qubit. Such interactions are available whenever qubits can be coupled to a shared harmonic oscillator, a situation that can be realized in many physical qubit implementations. For example, suitable interactions have already been realized for up to 14 qubits in ion traps. It should be possible to implement stabilizer codes for quantum error correction with a constant number of multi-qubit gates, in contrast to typical constructions with a number of two-qubit gates that increases as a function of N. The special case of finding the parity of N qubits only requires a small number of operations that is independent of N. This compares favorably to algorithms for computing the parity on conventional machines, which implies a genuine quantum advantage.

Phase transition of Boolean networks with partially nested canalizing functions

NASA Astrophysics Data System (ADS)

Jansen, Kayse; Matache, Mihaela Teodora

2013-07-01

We generate the critical condition for the phase transition of a Boolean network governed by partially nested canalizing functions for which a fraction of the inputs are canalizing, while the remaining non-canalizing inputs obey a complementary threshold Boolean function. Past studies have considered the stability of fully or partially nested canalizing functions paired with random choices of the complementary function. In some of those studies conflicting results were found with regard to the presence of chaotic behavior. Moreover, those studies focus mostly on ergodic networks in which initial states are assumed equally likely. We relax that assumption and find the critical condition for the sensitivity of the network under a non-ergodic scenario. We use the proposed mathematical model to determine parameter values for which phase transitions from order to chaos occur. We generate Derrida plots to show that the mathematical model matches the actual network dynamics. The phase transition diagrams indicate that both order and chaos can occur, and that certain parameters induce a larger range of values leading to order versus chaos. The edge-of-chaos curves are identified analytically and numerically. It is shown that the depth of canalization does not cause major dynamical changes once certain thresholds are reached; these thresholds are fairly small in comparison to the connectivity of the nodes.

Development of a computer-aided design software for dental splint in orthognathic surgery

NASA Astrophysics Data System (ADS)

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-12-01

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated.

Development of a computer-aided design software for dental splint in orthognathic surgery

PubMed Central

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-01-01

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated. PMID:27966601

Development of a computer-aided design software for dental splint in orthognathic surgery.

PubMed

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-12-14

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated.

Boolean Logic Tree of Label-Free Dual-Signal Electrochemical Aptasensor System for Biosensing, Three-State Logic Computation, and Keypad Lock Security Operation.

PubMed

Lu, Jiao Yang; Zhang, Xin Xing; Huang, Wei Tao; Zhu, Qiu Yan; Ding, Xue Zhi; Xia, Li Qiu; Luo, Hong Qun; Li, Nian Bing

2017-09-19

The most serious and yet unsolved problems of molecular logic computing consist in how to connect molecular events in complex systems into a usable device with specific functions and how to selectively control branchy logic processes from the cascading logic systems. This report demonstrates that a Boolean logic tree is utilized to organize and connect "plug and play" chemical events DNA, nanomaterials, organic dye, biomolecule, and denaturant for developing the dual-signal electrochemical evolution aptasensor system with good resettability for amplification detection of thrombin, controllable and selectable three-state logic computation, and keypad lock security operation. The aptasensor system combines the merits of DNA-functionalized nanoamplification architecture and simple dual-signal electroactive dye brilliant cresyl blue for sensitive and selective detection of thrombin with a wide linear response range of 0.02-100 nM and a detection limit of 1.92 pM. By using these aforementioned chemical events as inputs and the differential pulse voltammetry current changes at different voltages as dual outputs, a resettable three-input biomolecular keypad lock based on sequential logic is established. Moreover, the first example of controllable and selectable three-state molecular logic computation with active-high and active-low logic functions can be implemented and allows the output ports to assume a high impediment or nothing (Z) state in addition to the 0 and 1 logic levels, effectively controlling subsequent branchy logic computation processes. Our approach is helpful in developing the advanced controllable and selectable logic computing and sensing system in large-scale integration circuits for application in biomedical engineering, intelligent sensing, and control.

The value of less connected agents in Boolean networks

NASA Astrophysics Data System (ADS)

Epstein, Daniel; Bazzan, Ana L. C.

2013-11-01

In multiagent systems, agents often face binary decisions where one seeks to take either the minority or the majority side. Examples are minority and congestion games in general, i.e., situations that require coordination among the agents in order to depict efficient decisions. In minority games such as the El Farol Bar Problem, previous works have shown that agents may reach appropriate levels of coordination, mostly by looking at the history of past decisions. Not many works consider any kind of structure of the social network, i.e., how agents are connected. Moreover, when structure is indeed considered, it assumes some kind of random network with a given, fixed connectivity degree. The present paper departs from the conventional approach in some ways. First, it considers more realistic network topologies, based on preferential attachments. This is especially useful in social networks. Second, the formalism of random Boolean networks is used to help agents to make decisions given their attachments (for example acquaintances). This is coupled with a reinforcement learning mechanism that allows agents to select strategies that are locally and globally efficient. Third, we use agent-based modeling and simulation, a microscopic approach, which allows us to draw conclusions about individuals and/or classes of individuals. Finally, for the sake of illustration we use two different scenarios, namely the El Farol Bar Problem and a binary route choice scenario. With this approach we target systems that adapt dynamically to changes in the environment, including other adaptive decision-makers. Our results using preferential attachments and random Boolean networks are threefold. First we show that an efficient equilibrium can be achieved, provided agents do experimentation. Second, microscopic analysis show that influential agents tend to consider few inputs in their Boolean functions. Third, we have also conducted measurements related to network clustering and centrality that help to see how agents are organized.

Disparity between ultrasound and clinical findings in psoriatic arthritis.

PubMed

Husic, Rusmir; Gretler, Judith; Felber, Anja; Graninger, Winfried B; Duftner, Christina; Hermann, Josef; Dejaco, Christian

2014-08-01

To investigate the association between psoriatic arthritis (PsA)-specific clinical composite scores and ultrasound-verified pathology as well as comparison of clinical and ultrasound definitions of remission. We performed a prospective study on 70 consecutive PsA patients. Clinical assessments included components of Disease Activity Index for Psoriatic Arthritis (DAPSA) and the Composite Psoriatic Disease Activity Index (CPDAI). Minimal disease activity (MDA) and the following remission criteria were applied: CPDAI joint, entheses and dactylitis domains (CPDAI-JED)=0, DAPSA≤3.3, Boolean's remission definition and physician-judged remission (rem-phys). B-mode and power Doppler (PD-) ultrasound findings were semiquantitatively scored at 68 joints (evaluating synovia, peritendinous tissue, tendons and bony changes) and 14 entheses. Ultrasound remission and minimal ultrasound disease activity (MUDA) were defined as PD-score=0 and PD-score ≤1, respectively, at joints, peritendinous tissue, tendons and entheses. DAPSA but not CPDAI correlated with B-mode and PD-synovitis. Ultrasound signs of enthesitis, dactylitis, tenosynovitis and perisynovitis were not linked with clinical composites. Clinical remission or MDA was observed in 15.7% to 47.1% of PsA patients. Ultrasound remission and MUDA were present in 4.3% and 20.0% of patients, respectively. Joint and tendon-related PD-scores were higher in patients with active versus inactive disease according to CPDAI-JED, DAPSA, Boolean's and rem-phys, whereas no difference was observed regarding enthesitis and perisynovitis. DAPSA≤3.3 (OR 3.9, p=0.049) and Boolean's definition (OR 4.6, p=0.03) were more useful to predict MUDA than other remission criteria. PsA-specific composite scores partially reflect ultrasound findings. DAPSA and Boolean's remission definitions better identify MUDA patients than other clinical criteria. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

PubMed

Stoll, Gautier; Viara, Eric; Barillot, Emmanuel; Calzone, Laurence

2012-08-29

Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential equations on probability distributions. We developed a C++ software, MaBoSS, that is able to simulate such a system by applying Kinetic Monte-Carlo (or Gillespie algorithm) on the Boolean state space. This software, parallelized and optimized, computes the temporal evolution of probability distributions and estimates stationary distributions. Applications of the Boolean Kinetic Monte-Carlo are demonstrated for three qualitative models: a toy model, a published model of p53/Mdm2 interaction and a published model of the mammalian cell cycle. Our approach allows to describe kinetic phenomena which were difficult to handle in the original models. In particular, transient effects are represented by time dependent probability distributions, interpretable in terms of cell populations.

Development and Validation of Various Phenotyping Algorithms for Diabetes Mellitus Using Data from Electronic Health Records.

PubMed

Esteban, Santiago; Rodríguez Tablado, Manuel; Peper, Francisco; Mahumud, Yamila S; Ricci, Ricardo I; Kopitowski, Karin; Terrasa, Sergio

2017-01-01

Precision medicine requires extremely large samples. Electronic health records (EHR) are thought to be a cost-effective source of data for that purpose. Phenotyping algorithms help reduce classification errors, making EHR a more reliable source of information for research. Four algorithm development strategies for classifying patients according to their diabetes status (diabetics; non-diabetics; inconclusive) were tested (one codes-only algorithm; one boolean algorithm, four statistical learning algorithms and six stacked generalization meta-learners). The best performing algorithms within each strategy were tested on the validation set. The stacked generalization algorithm yielded the highest Kappa coefficient value in the validation set (0.95 95% CI 0.91, 0.98). The implementation of these algorithms allows for the exploitation of data from thousands of patients accurately, greatly reducing the costs of constructing retrospective cohorts for research.

MIRAP, microcomputer reliability analysis program

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

Jehee, J.N.T.

1989-01-01

A program for a microcomputer is outlined that can determine minimal cut sets from a specified fault tree logic. The speed and memory limitations of the microcomputers on which the program is implemented (Atari ST and IBM) are addressed by reducing the fault tree's size and by storing the cut set data on disk. Extensive well proven fault tree restructuring techniques, such as the identification of sibling events and of independent gate events, reduces the fault tree's size but does not alter its logic. New methods are used for the Boolean reduction of the fault tree logic. Special criteria formore » combining events in the 'AND' and 'OR' logic avoid the creation of many subsuming cut sets which all would cancel out due to existing cut sets. Figures and tables illustrates these methods. 4 refs., 5 tabs.« less

High-order cyclo-difference techniques: An alternative to finite differences

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.; Otto, John C.

1993-01-01

The summation-by-parts energy norm is used to establish a new class of high-order finite-difference techniques referred to here as 'cyclo-difference' techniques. These techniques are constructed cyclically from stable subelements, and require no numerical boundary conditions; when coupled with the simultaneous approximation term (SAT) boundary treatment, they are time asymptotically stable for an arbitrary hyperbolic system. These techniques are similar to spectral element techniques and are ideally suited for parallel implementation, but do not require special collocation points or orthogonal basis functions. The principal focus is on methods of sixth-order formal accuracy or less; however, these methods could be extended in principle to any arbitrary order of accuracy.

Synthetic space with arbitrary dimensions in a few rings undergoing dynamic modulation

NASA Astrophysics Data System (ADS)

Yuan, Luqi; Xiao, Meng; Lin, Qian; Fan, Shanhui

2018-03-01

We show that a single ring resonator undergoing dynamic modulation can be used to create a synthetic space with an arbitrary dimension. In such a system, the phases of the modulation can be used to create a photonic gauge potential in high dimensions. As an illustration of the implication of this concept, we show that the Haldane model, which exhibits nontrivial topology in two dimensions, can be implemented in the synthetic space using three rings. Our results point to a route toward exploring higher-dimensional topological physics in low-dimensional physical structures. The dynamics of photons in such synthetic spaces also provides a mechanism to control the spectrum of light.

Development of an in-fiber white-light interferometric distance sensor for absolute measurement of arbitrary small distances.

PubMed

Majumdar, Ayan; Huang, Haiying

2008-05-20

The fabrication, implementation, and evaluation of an in-fiber white-light interferometric distance sensor that is capable of measuring the absolute value of an arbitrary small distance are presented. Taking advantage of the mode-coupling effect of a long-period fiber grating, an additional cavity distance is added to the optical path difference of the distance sensor; therefore, it can generate a sufficient number of fringes for distance demodulation even if the free-space cavity distance is very small. It is experimentally verified that the distance sensor is capable of measuring small distances that are beyond the capability of a Fabry-Perot interferometric distance sensor.

Quantum mechanics in noninertial reference frames: Relativistic accelerations and fictitious forces

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

Klink, W.H., E-mail: william-klink@uiowa.edu; Wickramasekara, S., E-mail: wickrama@grinnell.edu

2016-06-15

One-particle systems in relativistically accelerating reference frames can be associated with a class of unitary representations of the group of arbitrary coordinate transformations, an extension of the Wigner–Bargmann definition of particles as the physical realization of unitary irreducible representations of the Poincaré group. Representations of the group of arbitrary coordinate transformations become necessary to define unitary operators implementing relativistic acceleration transformations in quantum theory because, unlike in the Galilean case, the relativistic acceleration transformations do not themselves form a group. The momentum operators that follow from these representations show how the fictitious forces in noninertial reference frames are generated inmore » quantum theory.« less

An angular biasing method using arbitrary convex polyhedra for Monte Carlo radiation transport calculations

DOE PAGES

Kulesza, Joel A.; Solomon, Clell J.; Kiedrowski, Brian C.

2018-01-02

This paper presents a new method for performing angular biasing in Monte Carlo radiation transport codes using arbitrary convex polyhedra to define regions of interest toward which to project particles (DXTRAN regions). The method is derived and is implemented using axis-aligned right parallelepipeds (AARPPs) and arbitrary convex polyhedra. Attention is also paid to possible numerical complications and areas for future refinement. A series of test problems are executed with void, purely absorbing, purely scattering, and 50% absorbing/50% scattering materials. For all test problems tally results using AARPP and polyhedral DXTRAN regions agree with analog and/or spherical DXTRAN results within statisticalmore » uncertainties. In cases with significant scattering the figure of merit (FOM) using AARPP or polyhedral DXTRAN regions is lower than with spherical regions despite the ability to closely fit the tally region. This is because spherical DXTRAN processing is computationally less expensive than AARPP or polyhedral DXTRAN processing. Thus, it is recommended that the speed of spherical regions be considered versus the ability to closely fit the tally region with an AARPP or arbitrary polyhedral region. It is also recommended that short calculations be made prior to final calculations to compare the FOM for the various DXTRAN geometries because of the influence of the scattering behavior.« less

Modeling of Complex Coupled Fluid-Structure Interaction Systems in Arbitrary Water Depth

DTIC Science & Technology

2009-01-01

basin. For the particle finite- element method ( PFEM ) near-field fluid model we completed: (4) the development of a fully-coupled fluid/flexible...method ( PFEM ) based framework for the ALE-RANS solver [1]. We presented the theory of ALE-RANS with a k- turbulence closure model and several numerical...implemented by PFEM (Task (4)). In this work a universal wall function (UWF) is introduced and implemented to more accurately predict the boundary

Boolean function applied to Mimosa pudica movements

PubMed Central

Friedman, Pedro

2011-01-01

Seismonastic or thigmonastic movements of Mimosa pudica L. is mostly because of the fast loss of water from swollen motor cells, resulting in temporary collapse of cells and quick curvature in the parts where these cells are located. Because of this, the plant has been much studied since the 18th century, leading us to think about the classical binomial stimulus-response (action-reaction) when compared to animals. Mechanic and electrical stimuli were used to investigate the analogy of mimosa branch with an artificial neuron model and to observe the action potential propagation through the mimosa branch. Boolean function applied to the mimosa branch in analogy with an artificial neuron model is one of the peculiarities of our hypothesis. PMID:21847029

Fisher information at the edge of chaos in random Boolean networks.

PubMed

Wang, X Rosalind; Lizier, Joseph T; Prokopenko, Mikhail

2011-01-01

We study the order-chaos phase transition in random Boolean networks (RBNs), which have been used as models of gene regulatory networks. In particular we seek to characterize the phase diagram in information-theoretic terms, focusing on the effect of the control parameters (activity level and connectivity). Fisher information, which measures how much system dynamics can reveal about the control parameters, offers a natural interpretation of the phase diagram in RBNs. We report that this measure is maximized near the order-chaos phase transitions in RBNs, since this is the region where the system is most sensitive to its parameters. Furthermore, we use this study of RBNs to clarify the relationship between Shannon and Fisher information measures.

Investigating Cell Criticality

NASA Astrophysics Data System (ADS)

Serra, R.; Villani, M.; Damiani, C.; Graudenzi, A.; Ingrami, P.; Colacci, A.

Random Boolean networks provide a way to give a precise meaning to the notion that living beings are in a critical state. Some phenomena which are observed in real biological systems (distribution of "avalanches" in gene knock-out experiments) can be modeled using random Boolean networks, and the results can be analytically proven to depend upon the Derrida parameter, which also determines whether the network is critical. By comparing observed and simulated data one can then draw inferences about the criticality of biological cells, although with some care because of the limited number of experimental observations. The relationship between the criticality of a single network and that of a set of interacting networks, which simulate a tissue or a bacterial colony, is also analyzed by computer simulations.

Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions.

PubMed

Qu, Xiangmeng; Wang, Shaopeng; Ge, Zhilei; Wang, Jianbang; Yao, Guangbao; Li, Jiang; Zuo, Xiaolei; Shi, Jiye; Song, Shiping; Wang, Lihua; Li, Li; Pei, Hao; Fan, Chunhai

2017-08-02

Programmable remodelling of cell surfaces enables high-precision regulation of cell behavior. In this work, we developed in vitro constructed DNA-based chemical reaction networks (CRNs) to program on-chip cell adhesion. We found that the RGD-functionalized DNA CRNs are entirely noninvasive when interfaced with the fluidic mosaic membrane of living cells. DNA toehold with different lengths could tunably alter the release kinetics of cells, which shows rapid release in minutes with the use of a 6-base toehold. We further demonstrated the realization of Boolean logic functions by using DNA strand displacement reactions, which include multi-input and sequential cell logic gates (AND, OR, XOR, and AND-OR). This study provides a highly generic tool for self-organization of biological systems.

Reliable computation from contextual correlations

NASA Astrophysics Data System (ADS)

Oestereich, André L.; Galvão, Ernesto F.

2017-12-01

An operational approach to the study of computation based on correlations considers black boxes with one-bit inputs and outputs, controlled by a limited classical computer capable only of performing sums modulo-two. In this setting, it was shown that noncontextual correlations do not provide any extra computational power, while contextual correlations were found to be necessary for the deterministic evaluation of nonlinear Boolean functions. Here we investigate the requirements for reliable computation in this setting; that is, the evaluation of any Boolean function with success probability bounded away from 1 /2 . We show that bipartite CHSH quantum correlations suffice for reliable computation. We also prove that an arbitrarily small violation of a multipartite Greenberger-Horne-Zeilinger noncontextuality inequality also suffices for reliable computation.

The pseudo-Boolean optimization approach to form the N-version software structure

NASA Astrophysics Data System (ADS)

Kovalev, I. V.; Kovalev, D. I.; Zelenkov, P. V.; Voroshilova, A. A.

2015-10-01

The problem of developing an optimal structure of N-version software system presents a kind of very complex optimization problem. This causes the use of deterministic optimization methods inappropriate for solving the stated problem. In this view, exploiting heuristic strategies looks more rational. In the field of pseudo-Boolean optimization theory, the so called method of varied probabilities (MVP) has been developed to solve problems with a large dimensionality. Some additional modifications of MVP have been made to solve the problem of N-version systems design. Those algorithms take into account the discovered specific features of the objective function. The practical experiments have shown the advantage of using these algorithm modifications because of reducing a search space.

Issues for a Model of Language Planning.

ERIC Educational Resources Information Center

Bamgbose, Ayo

1989-01-01

Examines the following issues as they relate to a model of language planning: (1) types of decisions (policy or implemental, higher- or lower-level, rational or arbitrary); (2) the planning mechanism; (3) the role of fact finding (prepolicy, preimplementation, and intraimplementation); (4) levels of planning; and (5) the nature of status versus…

An Elementary Algorithm to Evaluate Trigonometric Functions to High Precision

ERIC Educational Resources Information Center

Johansson, B. Tomas

2018-01-01

Evaluation of the cosine function is done via a simple Cordic-like algorithm, together with a package for handling arbitrary-precision arithmetic in the computer program Matlab. Approximations to the cosine function having hundreds of correct decimals are presented with a discussion around errors and implementation.

Current Issues in Reductions-in-Force.

ERIC Educational Resources Information Center

Caplan, Gerald A.

The practitioner advising a school board in connection with a reduction in force can appreciate that the board has great flexibility in implementing its decision. As long as the board's actions are not arbitrary, capricious, or pretextual, and they afford minimal due process protections to tenured teachers, the board's decisions will withstand…

Realisation of a holographic microlaser scalpel using a digital micromirror device

NASA Astrophysics Data System (ADS)

Zwick, Susanne; Warber, Michael; Haist, Tobias; Osten, Wolfgang

2007-06-01

Modern spatial light modulators (SLM) enable the generation of more or less arbitrary light fields in three dimensions. Such light fields can be used for different future applications in the field of biomedical optics. One example is the processing/cutting of biological material on a microscopic scale. By displaying computer generated holograms by suitable SLMs it is possible to ablate complex structures into three-dimensional objects without scanning with very high accuracy on a microscopic scale. To effectively cut biological materials by light, pulsed ultraviolet light is preferable. We will present a combined setup of a holographic laser scalpel using a digital micromirror device (DMD) and holographic optical tweezers using a liquid crystal display (LCD). The setup enables to move and cut or process micro-scaled objects like biological cells or tissue in three dimensions with high accuracy and without any mechanical movements just by changing the hologram displayed by the SLMs. We will show that holograms can be used to compensate aberrations implemented by the DMD or other optical components of the setup. Also we can generate arbitrary light fields like stripes, circles or arbitrary curves. Additionally we will present results for the fast optimization of holograms for the system. In particular we will show results obtained by implementing iterative Fourier transform based algorithms on a standard consumer graphics board (Nvidia 8800GLX). By this approach we are able to compute more than 360 complex 2D FFTs (512 × 512 pixels) per second with floating point precision.

Implementation of a block Lanczos algorithm for Eigenproblem solution of gyroscopic systems

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.; Lawson, Charles L.

1987-01-01

The details of implementation of a general numerical procedure developed for the accurate and economical computation of natural frequencies and associated modes of any elastic structure rotating along an arbitrary axis are described. A block version of the Lanczos algorithm is derived for the solution that fully exploits associated matrix sparsity and employs only real numbers in all relevant computations. It is also capable of determining multiple roots and proves to be most efficient when compared to other, similar, exisiting techniques.

On the photonic implementation of universal quantum gates, bell states preparation circuit and quantum LDPC encoders and decoders based on directional couplers and HNLF.

PubMed

Djordjevic, Ivan B

2010-04-12

The Bell states preparation circuit is a basic circuit required in quantum teleportation. We describe how to implement it in all-fiber technology. The basic building blocks for its implementation are directional couplers and highly nonlinear optical fiber (HNLF). Because the quantum information processing is based on delicate superposition states, it is sensitive to quantum errors. In order to enable fault-tolerant quantum computing the use of quantum error correction is unavoidable. We show how to implement in all-fiber technology encoders and decoders for sparse-graph quantum codes, and provide an illustrative example to demonstrate this implementation. We also show that arbitrary set of universal quantum gates can be implemented based on directional couplers and HNLFs.

Information processing in dendrites I. Input pattern generalisation.

PubMed

Gurney, K N

2001-10-01

In this paper and its companion, we address the question as to whether there are any general principles underlying information processing in the dendritic trees of biological neurons. In order to address this question, we make two assumptions. First, the key architectural feature of dendrites responsible for many of their information processing abilities is the existence of independent sub-units performing local non-linear processing. Second, any general functional principles operate at a level of abstraction in which neurons are modelled by Boolean functions. To accommodate these assumptions, we therefore define a Boolean model neuron-the multi-cube unit (MCU)-which instantiates the notion of the discrete functional sub-unit. We then use this model unit to explore two aspects of neural functionality: generalisation (in this paper) and processing complexity (in its companion). Generalisation is dealt with from a geometric viewpoint and is quantified using a new metric-the set of order parameters. These parameters are computed for threshold logic units (TLUs), a class of random Boolean functions, and MCUs. Our interpretation of the order parameters is consistent with our knowledge of generalisation in TLUs and with the lack of generalisation in randomly chosen functions. Crucially, the order parameters for MCUs imply that these functions possess a range of generalisation behaviour. We argue that this supports the general thesis that dendrites facilitate input pattern generalisation despite any local non-linear processing within functionally isolated sub-units.

Attractor-Based Obstructions to Growth in Homogeneous Cyclic Boolean Automata.

PubMed

Khan, Bilal; Cantor, Yuri; Dombrowski, Kirk

2015-11-01

We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each cell initially takes on an independently chosen Boolean value. During the lifetime of the organism, each cell updates its own value by responding to the presence (or absence) of diversity amongst its two neighbours' values. We show that if all cells eventually take a value of 0 (irrespective of their initial values) then the organism necessarily has a cell count that is a power of 2. In addition, the converse is also proved: if the number of cells in the organism is a proper power of 2, then no matter what the initial values of the cells are, eventually all cells take on a value of 0 and then cease to change further. We argue that such an absence of structure in the dynamical properties of the organism implies a lack of adaptiveness, and so is evolutionarily disadvantageous. It follows that as the organism doubles in size (say from m to 2m) it will necessarily encounter an intermediate size that is a proper power of 2, and suffers from low adaptiveness. Finally we show, through computational experiments, that one way an organism can grow to more than twice its size and still avoid passing through intermediate sizes that lack structural dynamics, is for the organism to depart from assumptions of homogeneity at the cellular level.

Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.

PubMed

Bandyopadhyay, Sanghamitra; Mallik, Saurav

2018-01-01

Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

Predictive computation of genomic logic processing functions in embryonic development

PubMed Central

Peter, Isabelle S.; Faure, Emmanuel; Davidson, Eric H.

2012-01-01

Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations. PMID:22927416

Attractor-Based Obstructions to Growth in Homogeneous Cyclic Boolean Automata

PubMed Central

Khan, Bilal; Cantor, Yuri; Dombrowski, Kirk

2016-01-01

We consider a synchronous Boolean organism consisting of N cells arranged in a circle, where each cell initially takes on an independently chosen Boolean value. During the lifetime of the organism, each cell updates its own value by responding to the presence (or absence) of diversity amongst its two neighbours’ values. We show that if all cells eventually take a value of 0 (irrespective of their initial values) then the organism necessarily has a cell count that is a power of 2. In addition, the converse is also proved: if the number of cells in the organism is a proper power of 2, then no matter what the initial values of the cells are, eventually all cells take on a value of 0 and then cease to change further. We argue that such an absence of structure in the dynamical properties of the organism implies a lack of adaptiveness, and so is evolutionarily disadvantageous. It follows that as the organism doubles in size (say from m to 2m) it will necessarily encounter an intermediate size that is a proper power of 2, and suffers from low adaptiveness. Finally we show, through computational experiments, that one way an organism can grow to more than twice its size and still avoid passing through intermediate sizes that lack structural dynamics, is for the organism to depart from assumptions of homogeneity at the cellular level. PMID:27660398

Diffraction of Harmonic Flexural Waves in a Cracked Elastic Plate Carrying Electrical Current

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Hasanyan, Davresh; Librescu, iviu; Qin, Zhanming

2005-01-01

The scattering effect of harmonic flexural waves at a through crack in an elastic plate carrying electrical current is investigated. In this context, the Kirchhoffean bending plate theory is extended as to include magnetoelastic interactions. An incident wave giving rise to bending moments symmetric about the longitudinal z-axis of the crack is applied. Fourier transform technique reduces the problem to dual integral equations, which are then cast to a system of two singular integral equations. Efficient numerical computation is implemented to get the bending moment intensity factor for arbitrary frequency of the incident wave and of arbitrary electrical current intensity. The asymptotic behaviour of the bending moment intensity factor is analysed and parametric studies are conducted.

The use of multisensor data for robotic applications

NASA Technical Reports Server (NTRS)

Abidi, M. A.; Gonzalez, R. C.

1990-01-01

The feasibility of realistic autonomous space manipulation tasks using multisensory information is shown through two experiments involving a fluid interchange system and a module interchange system. In both cases, autonomous location of the mating element, autonomous location of the guiding light target, mating, and demating of the system were performed. Specifically, vision-driven techniques were implemented to determine the arbitrary two-dimensional position and orientation of the mating elements as well as the arbitrary three-dimensional position and orientation of the light targets. The robotic system was also equipped with a force/torque sensor that continuously monitored the six components of force and torque exerted on the end effector. Using vision, force, torque, proximity, and touch sensors, the two experiments were completed successfully and autonomously.

Faithful Transfer Arbitrary Pure States with Mixed Resources

NASA Astrophysics Data System (ADS)

Luo, Ming-Xing; Li, Lin; Ma, Song-Ya; Chen, Xiu-Bo; Yang, Yi-Xian

2013-09-01

In this paper, we show that some special mixed quantum resource experience the same property of pure entanglement such as Bell state for quantum teleportation. It is shown that one mixed state and three bits of classical communication cost can be used to teleport one unknown qubit compared with two bits via pure resources. The schemes are easily implement with model physical techniques. Moreover, these resources are also optimal and typical for faithfully remotely prepare an arbitrary qubit, two-qubit and three-qubit states with mixed quantum resources. Our schemes are completed as same as those with pure quantum entanglement resources except only 1 bit additional classical communication cost required. The success probability is independent of the form of the mixed resources.

Algorithm for Identifying Erroneous Rain-Gauge Readings

NASA Technical Reports Server (NTRS)

Rickman, Doug

2005-01-01

An algorithm analyzes rain-gauge data to identify statistical outliers that could be deemed to be erroneous readings. Heretofore, analyses of this type have been performed in burdensome manual procedures that have involved subjective judgements. Sometimes, the analyses have included computational assistance for detecting values falling outside of arbitrary limits. The analyses have been performed without statistically valid knowledge of the spatial and temporal variations of precipitation within rain events. In contrast, the present algorithm makes it possible to automate such an analysis, makes the analysis objective, takes account of the spatial distribution of rain gauges in conjunction with the statistical nature of spatial variations in rainfall readings, and minimizes the use of arbitrary criteria. The algorithm implements an iterative process that involves nonparametric statistics.

Modeling gene regulatory networks: A network simplification algorithm

NASA Astrophysics Data System (ADS)

Ferreira, Luiz Henrique O.; de Castro, Maria Clicia S.; da Silva, Fabricio A. B.

2016-12-01

Boolean networks have been used for some time to model Gene Regulatory Networks (GRNs), which describe cell functions. Those models can help biologists to make predictions, prognosis and even specialized treatment when some disturb on the GRN lead to a sick condition. However, the amount of information related to a GRN can be huge, making the task of inferring its boolean network representation quite a challenge. The method shown here takes into account information about the interactome to build a network, where each node represents a protein, and uses the entropy of each node as a key to reduce the size of the network, allowing the further inferring process to focus only on the main protein hubs, the ones with most potential to interfere in overall network behavior.

Stability of Boolean multilevel networks.

PubMed

Cozzo, Emanuele; Arenas, Alex; Moreno, Yamir

2012-09-01

The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semiannealed approximation to study the stability properties of random Boolean networks in multiplex (multilayered) graphs. Our main finding is that the multilevel structure provides a mechanism for the stabilization of the dynamics of the whole system even when individual layers work on the chaotic regime, therefore identifying new ways of feedback between the structure and the dynamics of these systems. Our results point out the need for a conceptual transition from the physics of single-layered networks to the physics of multiplex networks. Finally, the fact that the coupling modifies the phase diagram and the critical conditions of the isolated layers suggests that interdependency can be used as a control mechanism.

Developing Interactive Educational Engineering Software for the World Wide Web with Java.

ERIC Educational Resources Information Center

Reed, John A.; Afjeh, Abdollah A.

1998-01-01

Illustrates the design and implementation of a Java applet for use in educational propulsion engineering curricula. The Java Gas Turbine Simulator applet provides an interactive graphical environment which allows the rapid, efficient construction and analysis of arbitrary gas turbine systems. The simulator can be easily accessed from the World…

GPU Accelerated Clustering for Arbitrary Shapes in Geoscience Data

NASA Astrophysics Data System (ADS)

Pankratius, V.; Gowanlock, M.; Rude, C. M.; Li, J. D.

2016-12-01

Clustering algorithms have become a vital component in intelligent systems for geoscience that helps scientists discover and track phenomena of various kinds. Here, we outline advances in Density-Based Spatial Clustering of Applications with Noise (DBSCAN) which detects clusters of arbitrary shape that are common in geospatial data. In particular, we propose a hybrid CPU-GPU implementation of DBSCAN and highlight new optimization approaches on the GPU that allows clustering detection in parallel while optimizing data transport during CPU-GPU interactions. We employ an efficient batching scheme between the host and GPU such that limited GPU memory is not prohibitive when processing large and/or dense datasets. To minimize data transfer overhead, we estimate the total workload size and employ an execution that generates optimized batches that will not overflow the GPU buffer. This work is demonstrated on space weather Total Electron Content (TEC) datasets containing over 5 million measurements from instruments worldwide, and allows scientists to spot spatially coherent phenomena with ease. Our approach is up to 30 times faster than a sequential implementation and therefore accelerates discoveries in large datasets. We acknowledge support from NSF ACI-1442997.

Continuous-scanning laser Doppler vibrometry: Extensions to arbitrary areas, multi-frequency and 3D capture

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

Weekes, B.; Ewins, D.; Acciavatti, F.

2014-05-27

To date, differing implementations of continuous scan laser Doppler vibrometry have been demonstrated by various academic institutions, but since the scan paths were defined using step or sine functions from function generators, the paths were typically limited to 1D line scans or 2D areas such as raster paths or Lissajous trajectories. The excitation was previously often limited to a single frequency due to the specific signal processing performed to convert the scan data into an ODS. In this paper, a configuration of continuous-scan laser Doppler vibrometry is demonstrated which permits scanning of arbitrary areas, with the benefit of allowing multi-frequency/broadbandmore » excitation. Various means of generating scan paths to inspect arbitrary areas are discussed and demonstrated. Further, full 3D vibration capture is demonstrated by the addition of a range-finding facility to the described configuration, and iteratively relocating a single scanning laser head. Here, the range-finding facility was provided by a Microsoft Kinect, an inexpensive piece of consumer electronics.« less

Improved surface-roughness scattering and mobility models for multi-gate FETs with arbitrary cross-section and biasing scheme

NASA Astrophysics Data System (ADS)

Lizzit, D.; Badami, O.; Specogna, R.; Esseni, D.

2017-06-01

We present a new model for surface roughness (SR) scattering in n-type multi-gate FETs (MuGFETs) and gate-all-around nanowire FETs with fairly arbitrary cross-sections, its implementation in a complete device simulator, and the validation against experimental electron mobility data. The model describes the SR scattering matrix elements as non-linear transformations of interface fluctuations, which strongly influences the root mean square value of the roughness required to reproduce experimental mobility data. Mobility simulations are performed via the deterministic solution of the Boltzmann transport equation for a 1D-electron gas and including the most relevant scattering mechanisms for electronic transport, such as acoustic, polar, and non-polar optical phonon scattering, Coulomb scattering, and SR scattering. Simulation results show the importance of accounting for arbitrary cross-sections and biasing conditions when compared to experimental data. We also discuss how mobility is affected by the shape of the cross-section as well as by its area in gate-all-around and tri-gate MuGFETs.

Universal scheme for finite-probability perfect transfer of arbitrary multispin states through spin chains

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

Man, Zhong-Xiao, E-mail: zxman@mail.qfnu.edu.cn; An, Nguyen Ba, E-mail: nban@iop.vast.ac.vn; Xia, Yun-Jie, E-mail: yjxia@mail.qfnu.edu.cn

In combination with the theories of open system and quantum recovering measurement, we propose a quantum state transfer scheme using spin chains by performing two sequential operations: a projective measurement on the spins of ‘environment’ followed by suitably designed quantum recovering measurements on the spins of interest. The scheme allows perfect transfer of arbitrary multispin states through multiple parallel spin chains with finite probability. Our scheme is universal in the sense that it is state-independent and applicable to any model possessing spin–spin interactions. We also present possible methods to implement the required measurements taking into account the current experimental technologies.more » As applications, we consider two typical models for which the probabilities of perfect state transfer are found to be reasonably high at optimally chosen moments during the time evolution. - Highlights: • Scheme that can achieve perfect quantum state transfer is devised. • The scheme is state-independent and applicable to any spin-interaction models. • The scheme allows perfect transfer of arbitrary multispin states. • Applications to two typical models are considered in detail.« less

Optical arbitrary waveform generation based on multi-wavelength semiconductor fiber ring laser

NASA Astrophysics Data System (ADS)

Li, Peili; Ma, Xiaolu; Shi, Weihua; Xu, Enming

2017-09-01

A new scheme of generating optical arbitrary waveforms based on multi-wavelength semiconductor fiber ring laser (SFRL) is proposed. In this novel scheme, a wide and flat optical frequency comb (OFC) is provided directly by multi-wavelength SFRL, whose central frequency and comb spacing are tunable. OFC generation, de-multiplexing, amplitude and phase modulation, and multiplexing are implementing in an intensity and phase tunable comb filter, as induces the merits of high spectral coherence, satisfactory waveform control and low system loss. By using the mode couple theory and the transfer matrix method, the theoretical model of the scheme is established. The impacts of amplitude control, phase control, number of spectral line, and injection current of semiconductor optical amplifier (SOA) on the waveform similarity are studied using the theoretical model. The results show that, amplitude control and phase control error should be smaller than 1% and 0.64% respectively to achieve high similarity. The similarity of the waveform is improved with the increase of the number of spectral line. When the injection current of SOA is in a certain range, the optical arbitrary waveform reaches a high similarity.

Virtual photons in imaginary time: Computing exact Casimir forces via standard numerical electromagnetism techniques

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

Rodriguez, Alejandro; Ibanescu, Mihai; Joannopoulos, J. D.

2007-09-15

We describe a numerical method to compute Casimir forces in arbitrary geometries, for arbitrary dielectric and metallic materials, with arbitrary accuracy (given sufficient computational resources). Our approach, based on well-established integration of the mean stress tensor evaluated via the fluctuation-dissipation theorem, is designed to directly exploit fast methods developed for classical computational electromagnetism, since it only involves repeated evaluation of the Green's function for imaginary frequencies (equivalently, real frequencies in imaginary time). We develop the approach by systematically examining various formulations of Casimir forces from the previous decades and evaluating them according to their suitability for numerical computation. We illustratemore » our approach with a simple finite-difference frequency-domain implementation, test it for known geometries such as a cylinder and a plate, and apply it to new geometries. In particular, we show that a pistonlike geometry of two squares sliding between metal walls, in both two and three dimensions with both perfect and realistic metallic materials, exhibits a surprising nonmonotonic ''lateral'' force from the walls.« less

Biosensors with Built-In Biomolecular Logic Gates for Practical Applications

PubMed Central

Lai, Yu-Hsuan; Sun, Sin-Cih; Chuang, Min-Chieh

2014-01-01

Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems. PMID:25587423

Integrating query of relational and textual data in clinical databases: a case study.

PubMed

Fisk, John M; Mutalik, Pradeep; Levin, Forrest W; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

2003-01-01

The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Results are relevance-ranked using either "total documents per patient" or "report type weighting." Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers.

Using Volunteer Computing to Study Some Features of Diagonal Latin Squares

NASA Astrophysics Data System (ADS)

Vatutin, Eduard; Zaikin, Oleg; Kochemazov, Stepan; Valyaev, Sergey

2017-12-01

In this research, the study concerns around several features of diagonal Latin squares (DLSs) of small order. Authors of the study suggest an algorithm for computing minimal and maximal numbers of transversals of DLSs. According to this algorithm, all DLSs of a particular order are generated, and for each square all its transversals and diagonal transversals are constructed. The algorithm was implemented and applied to DLSs of order at most 7 on a personal computer. The experiment for order 8 was performed in the volunteer computing project Gerasim@home. In addition, the problem of finding pairs of orthogonal DLSs of order 10 was considered and reduced to Boolean satisfiability problem. The obtained problem turned out to be very hard, therefore it was decomposed into a family of subproblems. In order to solve the problem, the volunteer computing project SAT@home was used. As a result, several dozen pairs of described kind were found.

Post optimization paradigm in maximum 3-satisfiability logic programming

NASA Astrophysics Data System (ADS)

Mansor, Mohd. Asyraf; Sathasivam, Saratha; Kasihmuddin, Mohd Shareduwan Mohd

2017-08-01

Maximum 3-Satisfiability (MAX-3SAT) is a counterpart of the Boolean satisfiability problem that can be treated as a constraint optimization problem. It deals with a conundrum of searching the maximum number of satisfied clauses in a particular 3-SAT formula. This paper presents the implementation of enhanced Hopfield network in hastening the Maximum 3-Satisfiability (MAX-3SAT) logic programming. Four post optimization techniques are investigated, including the Elliot symmetric activation function, Gaussian activation function, Wavelet activation function and Hyperbolic tangent activation function. The performances of these post optimization techniques in accelerating MAX-3SAT logic programming will be discussed in terms of the ratio of maximum satisfied clauses, Hamming distance and the computation time. Dev-C++ was used as the platform for training, testing and validating our proposed techniques. The results depict the Hyperbolic tangent activation function and Elliot symmetric activation function can be used in doing MAX-3SAT logic programming.

An algorithmic approach to solving polynomial equations associated with quantum circuits

NASA Astrophysics Data System (ADS)

Gerdt, V. P.; Zinin, M. V.

2009-12-01

In this paper we present two algorithms for reducing systems of multivariate polynomial equations over the finite field F 2 to the canonical triangular form called lexicographical Gröbner basis. This triangular form is the most appropriate for finding solutions of the system. On the other hand, the system of polynomials over F 2 whose variables also take values in F 2 (Boolean polynomials) completely describes the unitary matrix generated by a quantum circuit. In particular, the matrix itself can be computed by counting the number of solutions (roots) of the associated polynomial system. Thereby, efficient construction of the lexicographical Gröbner bases over F 2 associated with quantum circuits gives a method for computing their circuit matrices that is alternative to the direct numerical method based on linear algebra. We compare our implementation of both algorithms with some other software packages available for computing Gröbner bases over F 2.

Markov chain algorithms: a template for building future robust low-power systems

PubMed Central

Deka, Biplab; Birklykke, Alex A.; Duwe, Henry; Mansinghka, Vikash K.; Kumar, Rakesh

2014-01-01

Although computational systems are looking towards post CMOS devices in the pursuit of lower power, the expected inherent unreliability of such devices makes it difficult to design robust systems without additional power overheads for guaranteeing robustness. As such, algorithmic structures with inherent ability to tolerate computational errors are of significant interest. We propose to cast applications as stochastic algorithms based on Markov chains (MCs) as such algorithms are both sufficiently general and tolerant to transition errors. We show with four example applications—Boolean satisfiability, sorting, low-density parity-check decoding and clustering—how applications can be cast as MC algorithms. Using algorithmic fault injection techniques, we demonstrate the robustness of these implementations to transition errors with high error rates. Based on these results, we make a case for using MCs as an algorithmic template for future robust low-power systems. PMID:24842030

Non-Boolean computing with nanomagnets for computer vision applications

NASA Astrophysics Data System (ADS)

Bhanja, Sanjukta; Karunaratne, D. K.; Panchumarthy, Ravi; Rajaram, Srinath; Sarkar, Sudeep

2016-02-01

The field of nanomagnetism has recently attracted tremendous attention as it can potentially deliver low-power, high-speed and dense non-volatile memories. It is now possible to engineer the size, shape, spacing, orientation and composition of sub-100 nm magnetic structures. This has spurred the exploration of nanomagnets for unconventional computing paradigms. Here, we harness the energy-minimization nature of nanomagnetic systems to solve the quadratic optimization problems that arise in computer vision applications, which are computationally expensive. By exploiting the magnetization states of nanomagnetic disks as state representations of a vortex and single domain, we develop a magnetic Hamiltonian and implement it in a magnetic system that can identify the salient features of a given image with more than 85% true positive rate. These results show the potential of this alternative computing method to develop a magnetic coprocessor that might solve complex problems in fewer clock cycles than traditional processors.

Conceptual search in electronic patient record.

PubMed

Baud, R H; Lovis, C; Ruch, P; Rassinoux, A M

2001-01-01

Search by content in a large corpus of free texts in the medical domain is, today, only partially solved. The so-called GREP approach (Get Regular Expression and Print), based on highly efficient string matching techniques, is subject to inherent limitations, especially its inability to recognize domain specific knowledge. Such methods oblige the user to formulate his or her query in a logical Boolean style; if this constraint is not fulfilled, the results are poor. The authors present an enhancement to string matching search by the addition of a light conceptual model behind the word lexicon. The new system accepts any sentence as a query and radically improves the quality of results. Efficiency regarding execution time is obtained at the expense of implementing advanced indexing algorithms in a pre-processing phase. The method is described and commented and a brief account of the results illustrates this paper.

Building the 3D Geological Model of Wall Rock of Salt Caverns Based on Integration Method of Multi-source data

NASA Astrophysics Data System (ADS)

Yongzhi, WANG; hui, WANG; Lixia, LIAO; Dongsen, LI

2017-02-01

In order to analyse the geological characteristics of salt rock and stability of salt caverns, rough three-dimensional (3D) models of salt rock stratum and the 3D models of salt caverns on study areas are built by 3D GIS spatial modeling technique. During implementing, multi-source data, such as basic geographic data, DEM, geological plane map, geological section map, engineering geological data, and sonar data are used. In this study, the 3D spatial analyzing and calculation methods, such as 3D GIS intersection detection method in three-dimensional space, Boolean operations between three-dimensional space entities, three-dimensional space grid discretization, are used to build 3D models on wall rock of salt caverns. Our methods can provide effective calculation models for numerical simulation and analysis of the creep characteristics of wall rock in salt caverns.

The scalable implementation of quantum walks using classical light

NASA Astrophysics Data System (ADS)

Goyal, Sandeep K.; Roux, F. S.; Forbes, Andrew; Konrad, Thomas

2014-02-01

A quantum walk is the quantum analog of the classical random walks. Despite their simple structure they form a universal platform to implement any algorithm of quantum computation. However, it is very hard to realize quantum walks with a sufficient number of iterations in quantum systems due to their sensitivity to environmental influences and subsequent loss of coherence. Here we present a scalable implementation scheme for one-dimensional quantum walks for arbitrary number of steps using the orbital angular momentum modes of classical light beams. Furthermore, we show that using the same setup with a minor adjustment we can also realize electric quantum walks.

Scan-Based Implementation of JPEG 2000 Extensions

NASA Technical Reports Server (NTRS)

Rountree, Janet C.; Webb, Brian N.; Flohr, Thomas J.; Marcellin, Michael W.

2001-01-01

JPEG 2000 Part 2 (Extensions) contains a number of technologies that are of potential interest in remote sensing applications. These include arbitrary wavelet transforms, techniques to limit boundary artifacts in tiles, multiple component transforms, and trellis-coded quantization (TCQ). We are investigating the addition of these features to the low-memory (scan-based) implementation of JPEG 2000 Part 1. A scan-based implementation of TCQ has been realized and tested, with a very small performance loss as compared with the full image (frame-based) version. A proposed amendment to JPEG 2000 Part 2 will effect the syntax changes required to make scan-based TCQ compatible with the standard.

Understanding genetic regulatory networks

NASA Astrophysics Data System (ADS)

Kauffman, Stuart

2003-04-01

Random Boolean networks (RBM) were introduced about 35 years ago as first crude models of genetic regulatory networks. RBNs are comprised of N on-off genes, connected by a randomly assigned regulatory wiring diagram where each gene has K inputs, and each gene is controlled by a randomly assigned Boolean function. This procedure samples at random from the ensemble of all possible NK Boolean networks. The central ideas are to study the typical, or generic properties of this ensemble, and see 1) whether characteristic differences appear as K and biases in Boolean functions are introducted, and 2) whether a subclass of this ensemble has properties matching real cells. Such networks behave in an ordered or a chaotic regime, with a phase transition, "the edge of chaos" between the two regimes. Networks with continuous variables exhibit the same two regimes. Substantial evidence suggests that real cells are in the ordered regime. A key concept is that of an attractor. This is a reentrant trajectory of states of the network, called a state cycle. The central biological interpretation is that cell types are attractors. A number of properties differentiate the ordered and chaotic regimes. These include the size and number of attractors, the existence in the ordered regime of a percolating "sea" of genes frozen in the on or off state, with a remainder of isolated twinkling islands of genes, a power law distribution of avalanches of gene activity changes following perturbation to a single gene in the ordered regime versus a similar power law distribution plus a spike of enormous avalanches of gene changes in the chaotic regime, and the existence of branching pathway of "differentiation" between attractors induced by perturbations in the ordered regime. Noise is serious issue, since noise disrupts attractors. But numerical evidence suggests that attractors can be made very stable to noise, and meanwhile, metaplasias may be a biological manifestation of noise. As we learn more about the wiring diagram and constraints on rules controlling real genes, we can build refined ensembles reflecting these properties, study the generic properties of the refined ensembles, and hope to gain insight into the dynamics of real cells.

An end-to-end workflow for engineering of biological networks from high-level specifications.

PubMed

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

2012-08-17

We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

Fredkin and Toffoli Gates Implemented in Oregonator Model of Belousov-Zhabotinsky Medium

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

A thin-layer Belousov-Zhabotinsky (BZ) medium is a powerful computing device capable for implementing logical circuits, memory, image processors, robot controllers, and neuromorphic architectures. We design the reversible logical gates — Fredkin gate and Toffoli gate — in a BZ medium network of excitable channels with subexcitable junctions. Local control of the BZ medium excitability is an important feature of the gates’ design. An excitable thin-layer BZ medium responds to a localized perturbation with omnidirectional target or spiral excitation waves. A subexcitable BZ medium responds to an asymmetric perturbation by producing traveling localized excitation wave-fragments similar to dissipative solitons. We employ interactions between excitation wave-fragments to perform the computation. We interpret the wave-fragments as values of Boolean variables. The presence of a wave-fragment at a given site of a circuit represents the logical truth, absence of the wave-fragment — logically false. Fredkin gate consists of ten excitable channels intersecting at 11 junctions, eight of which are subexcitable. Toffoli gate consists of six excitable channels intersecting at six junctions, four of which are subexcitable. The designs of the gates are verified using numerical integration of two-variable Oregonator equations.

Generalized Optical Theorem Detection in Random and Complex Media

NASA Astrophysics Data System (ADS)

Tu, Jing

The problem of detecting changes of a medium or environment based on active, transmit-plus-receive wave sensor data is at the heart of many important applications including radar, surveillance, remote sensing, nondestructive testing, and cancer detection. This is a challenging problem because both the change or target and the surrounding background medium are in general unknown and can be quite complex. This Ph.D. dissertation presents a new wave physics-based approach for the detection of targets or changes in rather arbitrary backgrounds. The proposed methodology is rooted on a fundamental result of wave theory called the optical theorem, which gives real physical energy meaning to the statistics used for detection. This dissertation is composed of two main parts. The first part significantly expands the theory and understanding of the optical theorem for arbitrary probing fields and arbitrary media including nonreciprocal media, active media, as well as time-varying and nonlinear scatterers. The proposed formalism addresses both scalar and full vector electromagnetic fields. The second contribution of this dissertation is the application of the optical theorem to change detection with particular emphasis on random, complex, and active media, including single frequency probing fields and broadband probing fields. The first part of this work focuses on the generalization of the existing theoretical repertoire and interpretation of the scalar and electromagnetic optical theorem. Several fundamental generalizations of the optical theorem are developed. A new theory is developed for the optical theorem for scalar fields in nonhomogeneous media which can be bounded or unbounded. The bounded media context is essential for applications such as intrusion detection and surveillance in enclosed environments such as indoor facilities, caves, tunnels, as well as for nondestructive testing and communication systems based on wave-guiding structures. The developed scalar optical theorem theory applies to arbitrary lossless backgrounds and quite general probing fields including near fields which play a key role in super-resolution imaging. The derived formulation holds for arbitrary passive scatterers, which can be dissipative, as well as for the more general class of active scatterers which are composed of a (passive) scatterer component and an active, radiating (antenna) component. Furthermore, the generalization of the optical theorem to active scatterers is relevant to many applications such as surveillance of active targets including certain cloaks, invisible scatterers, and wireless communications. The latter developments have important military applications. The derived theoretical framework includes the familiar real power optical theorem describing power extinction due to both dissipation and scattering as well as a reactive optical theorem related to the reactive power changes. Meanwhile, the developed approach naturally leads to three optical theorem indicators or statistics, which can be used to detect changes or targets in unknown complex media. In addition, the optical theorem theory is generalized in the time domain so that it applies to arbitrary full vector fields, and arbitrary media including anisotropic media, nonreciprocal media, active media, as well as time-varying and nonlinear scatterers. The second component of this Ph.D. research program focuses on the application of the optical theorem to change detection. Three different forms of indicators or statistics are developed for change detection in unknown background media: a real power optical theorem detector, a reactive power optical theorem detector, and a total apparent power optical theorem detector. No prior knowledge is required of the background or the change or target. The performance of the three proposed optical theorem detectors is compared with the classical energy detector approach for change detection. The latter uses a mathematical or functional energy while the optical theorem detectors are based on real physical energy. For reference, the optical theorem detectors are also compared with the matched filter approach which (unlike the optical theorem detectors) assumes perfect target and medium information. The practical implementation of the optical theorem detectors is based for certain random and complex media on the exploitation of time reversal focusing ideas developed in the past 20 years in electromagnetics and acoustics. In the final part of the dissertation, we also discuss the implementation of the optical theorem sensors for one-dimensional propagation systems such as transmission lines. We also present a new generalized likelihood ratio test for detection that exploits a prior data constraint based on the optical theorem. Finally, we also address the practical implementation of the optical theorem sensors for optical imaging systems, by means of holography. The later is the first holographic implementation the optical theorem for arbitrary scenes and targets.

Application of an Arbitrary Lagrangian Eulerian Method to Describe High Velocity Gas-Particle Flow Behavior

DTIC Science & Technology

2011-09-01

applied in this work was based on some of the standard definitions of soil constitutive properties as found in, e.g., Chen and Baladi [20], and...Livermore, CA. [20] Chen, W. F., and Baladi , G. Y., 1985. Soil Plasticity: Theory and Implementation. Elsevier Science, New York. [21] Zimmerman, H.D

A hardware-oriented algorithm for floating-point function generation

NASA Technical Reports Server (NTRS)

O'Grady, E. Pearse; Young, Baek-Kyu

1991-01-01

An algorithm is presented for performing accurate, high-speed, floating-point function generation for univariate functions defined at arbitrary breakpoints. Rapid identification of the breakpoint interval, which includes the input argument, is shown to be the key operation in the algorithm. A hardware implementation which makes extensive use of read/write memories is used to illustrate the algorithm.

Non-local classical optical correlation and implementing analogy of quantum teleportation

PubMed Central

Sun, Yifan; Song, Xinbing; Qin, Hongwei; Zhang, Xiong; Yang, Zhenwei; Zhang, Xiangdong

2015-01-01

This study reports an experimental realization of non-local classical optical correlation from the Bell's measurement used in tests of quantum non-locality. Based on such a classical Einstein–Podolsky–Rosen optical correlation, a classical analogy has been implemented to the true meaning of quantum teleportation. In the experimental teleportation protocol, the initial teleported information can be unknown to anyone and the information transfer can happen over arbitrary distances. The obtained results give novel insight into quantum physics and may open a new field of applications in quantum information. PMID:25779977

A design optimization process for Space Station Freedom

NASA Technical Reports Server (NTRS)

Chamberlain, Robert G.; Fox, George; Duquette, William H.

1990-01-01

The Space Station Freedom Program is used to develop and implement a process for design optimization. Because the relative worth of arbitrary design concepts cannot be assessed directly, comparisons must be based on designs that provide the same performance from the point of view of station users; such designs can be compared in terms of life cycle cost. Since the technology required to produce a space station is widely dispersed, a decentralized optimization process is essential. A formulation of the optimization process is provided and the mathematical models designed to facilitate its implementation are described.

Electrical Circuits in the Mathematics/Computer Science Classroom.

ERIC Educational Resources Information Center

McMillan, Robert D.

1988-01-01

Shows how, with little or no electrical background, students can apply Boolean algebra concepts to design and build integrated electrical circuits in the classroom that will reinforce important ideas in mathematics. (PK)

Topological Aspects of Information Retrieval.

ERIC Educational Resources Information Center

Egghe, Leo; Rousseau, Ronald

1998-01-01

Discusses topological aspects of theoretical information retrieval, including retrieval topology; similarity topology; pseudo-metric topology; document spaces as topological spaces; Boolean information retrieval as a subsystem of any topological system; and proofs of theorems. (LRW)

Combinatorial optimization in foundry practice

NASA Astrophysics Data System (ADS)

Antamoshkin, A. N.; Masich, I. S.

2016-04-01

The multicriteria mathematical model of foundry production capacity planning is suggested in the paper. The model is produced in terms of pseudo-Boolean optimization theory. Different search optimization methods were used to solve the obtained problem.

Defining of the BDX930 Assembly Language

NASA Technical Reports Server (NTRS)

Boyer, R. S.; Moore, J. S.

1983-01-01

A definition of the BDX930 assembly language is presented. Various definition problems and suggested solutions are included. A class of defined recognizers based on boolean valued nowrecursive functions is employed in preprocessing.

Application of a Discrete Nonlinear Spectral Model to Ideal Cases of Wind Wave Generation.

DTIC Science & Technology

1982-04-01

WRITE (6965)) bBD ODRM4T (IHII C SKI ’> 3 LINS i AND WRITE PLOT TITLE (IDOCHAR S PER LINE t 10 LINES AXI4CH-,(NClkR*9) /10 dRJTE (660) (TJL..EfI),I-I...A*CaGE.D.)JPP-J>P 𔃻 I F ( 8 D Do)) jpp-j P?+2 MiFPPeE)’i)&O TO 44 73 40JT-NPr(NIN,JPP) ;o TD (72, 14,7b,7BhNOUT 44 IF(A*3)q46q4b47 46 JPP-2 ;0 TO 73...EXTEZNAL FJNrI3N LAND IJS 13 THE BOOLEAN I.EoLDGICAL$ AND 01’ Td C FULLWORD INTEGCRS. C EXTEtNAL FJN:TION LOR, I,JS 1)7 THE BOOLEAN OR OF TWO FULLWORD

Analog Approach to Constraint Satisfaction Enabled by Spin Orbit Torque Magnetic Tunnel Junctions.

PubMed

Wijesinghe, Parami; Liyanagedera, Chamika; Roy, Kaushik

2018-05-02

Boolean satisfiability (k-SAT) is an NP-complete (k ≥ 3) problem that constitute one of the hardest classes of constraint satisfaction problems. In this work, we provide a proof of concept hardware based analog k-SAT solver, that is built using Magnetic Tunnel Junctions (MTJs). The inherent physics of MTJs, enhanced by device level modifications, is harnessed here to emulate the intricate dynamics of an analog satisfiability (SAT) solver. In the presence of thermal noise, the MTJ based system can successfully solve Boolean satisfiability problems. Most importantly, our results exhibit that, the proposed MTJ based hardware SAT solver is capable of finding a solution to a significant fraction (at least 85%) of hard 3-SAT problems, within a time that has a polynomial relationship with the number of variables(<50).

Remission of rheumatoid arthritis and potential determinants: a national multi-center cross-sectional survey.

PubMed

Wang, Guan-Ying; Zhang, Sa-Li; Wang, Xiu-Ru; Feng, Min; Li, Chun; An, Yuan; Li, Xiao-Feng; Wang, Li-Zhi; Wang, Cai-Hong; Wang, Yong-Fu; Yang, Rong; Yan, Hui-Ming; Wang, Guo-Chun; Lu, Xin; Liu, Xia; Zhu, Ping; Chen, Li-Na; Jin, Hong-Tao; Liu, Jin-Ting; Guo, Hui-Fang; Chen, Hai-Ying; Xie, Jian-Li; Wei, Ping; Wang, Jun-Xiang; Liu, Xiang-Yuan; Sun, Lin; Cui, Liu-Fu; Shu, Rong; Liu, Bai-Lu; Yu, Ping; Zhang, Zhuo-Li; Li, Guang-Tao; Li, Zhen-Bin; Yang, Jing; Li, Jun-Fang; Jia, Bin; Zhang, Feng-Xiao; Tao, Jie-Mei; Lin, Jin-Ying; Wei, Mei-Qiu; Liu, Xiao-Min; Ke, Dan; Hu, Shao-Xian; Ye, Cong; Han, Shu-Ling; Yang, Xiu-Yan; Li, Hao; Huang, Ci-Bo; Gao, Ming; Lai, Bei; Cheng, Yong-Jing; Li, Xing-Fu; Song, Li-Jun; Yu, Xiao-Xia; Wang, Ai-Xue; Wu, Li-Jun; Wang, Yan-Hua; He, Lan; Sun, Wen-Wen; Gong, Lu; Wang, Xiao-Yuan; Wang, Yi; Zhao, Yi; Li, Xiao-Xia; Wang, Yan; Zhang, Yan; Su, Yin; Zhang, Chun-Fang; Mu, Rong; Li, Zhan-Guo

2015-02-01

The aim of this study is to investigate the remission rate of rheumatoid arthritis (RA) in China and identify its potential determinants. A multi-center cross-sectional study was conducted from July 2009 to January 2012. Data were collected by face-to-face interviews of the rheumatology outpatients in 28 tertiary hospitals in China. The remission rates were calculated in 486 RA patients according to different definitions of remission: the Disease Activity Score in 28 joints (DAS28), the Simplified Disease Activity Index (SDAI), the Clinical Disease Activity Index (CDAI), and the American College of Rheumatology/European League Against Rheumatism (ACR/EULAR) Boolean definition. Potential determinants of RA remission were assessed by univariate and multivariate analyses. The remission rates of RA from this multi-center cohort were 8.6% (DAS28), 8.4% (SDAI), 8.2% (CDAI), and 6.8% (Boolean), respectively. Favorable factors associated with remission were: low Health Assessment Questionnaire (HAQ) score, absence of rheumatoid factor (RF) and anti-cyclic citrullinated peptide (anti-CCP), and treatment of methotrexate (MTX) and hydroxychloroquine (HCQ). Younger age was also predictive for the DAS28 and the Boolean remission. Multivariate analyses revealed a low HAQ score, the absence of anti-CCP, and the treatment with HCQ as independent determinants of remission. The clinical remission rate of RA patients was low in China. A low HAQ score, the absence of anti-CCP, and HCQ were significant independent determinants for RA remission.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

Psychological state is related to the remission of the Boolean-based definition of patient global assessment in patients with rheumatoid arthritis.

PubMed

Fusama, Mie; Miura, Yasushi; Yukioka, Kumiko; Kuroiwa, Takanori; Yukioka, Chikako; Inoue, Miyako; Nakanishi, Tae; Murata, Norikazu; Takai, Noriko; Higashi, Kayoko; Kuritani, Taro; Maeda, Keiji; Sano, Hajime; Yukioka, Masao; Nakahara, Hideko

2015-09-01

To evaluate whether the psychological state is related to the Boolean-based definition of patient global assessment (PGA) remission in patients with rheumatoid arthritis (RA). Patients with RA who met the criteria of swollen joint count (SJC) ≤ 1, tender joint count (TJC) ≤ 1 and C-reactive protein (CRP) ≤ 1 were divided into two groups, PGA remission group (PGA ≤ 1 cm) and non-remission group (PGA > 1 cm). Anxiety was evaluated utilizing the Hospital Anxiety and Depression Scale-Anxiety (HADS-A), while depression was evaluated with HADS-Depression (HADS-D) and the Center for Epidemiologic Studies Depression Scale (CES-D). Comparison analyses were done between the PGA remission and non-remission groups in HADS-A, HADS-D and CES-D. Seventy-eight patients met the criteria for SJC ≤ 1, TJC ≤ 1 and CRP ≤ 1. There were no significant differences between the PGA remission group (n = 45) and the non-remission group (n = 33) in age, sex, disease duration and Steinbrocker's class and stage. HADS-A, HADS-D and CES-D scores were significantly lower in the PGA remission group. Patients with RA who did not meet the PGA remission criteria despite good disease condition were in a poorer psychological state than those who satisfied the Boolean-based definition of clinical remission. Psychological support might be effective for improvement of PGA, resulting in the attainment of true remission.

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

Bartkiewicz, Karol; Miranowicz, Adam

We find an optimal quantum cloning machine, which clones qubits of arbitrary symmetrical distribution around the Bloch vector with the highest fidelity. The process is referred to as phase-independent cloning in contrast to the standard phase-covariant cloning for which an input qubit state is a priori better known. We assume that the information about the input state is encoded in an arbitrary axisymmetric distribution (phase function) on the Bloch sphere of the cloned qubits. We find analytical expressions describing the optimal cloning transformation and fidelity of the clones. As an illustration, we analyze cloning of qubit state described by themore » von Mises-Fisher and Brosseau distributions. Moreover, we show that the optimal phase-independent cloning machine can be implemented by modifying the mirror phase-covariant cloning machine for which quantum circuits are known.« less

Mutual potential between two rigid bodies with arbitrary shapes and mass distributions

NASA Astrophysics Data System (ADS)

Hou, Xiyun; Scheeres, Daniel J.; Xin, Xiaosheng

2017-03-01

Formulae to compute the mutual potential, force, and torque between two rigid bodies are given. These formulae are expressed in Cartesian coordinates using inertia integrals. They are valid for rigid bodies with arbitrary shapes and mass distributions. By using recursive relations, these formulae can be easily implemented on computers. Comparisons with previous studies show their superiority in computation speed. Using the algorithm as a tool, the planar problem of two ellipsoids is studied. Generally, potential truncated at the second order is good enough for a qualitative description of the mutual dynamics. However, for ellipsoids with very large non-spherical terms, higher order terms of the potential should be considered, at the cost of a higher computational cost. Explicit formulae of the potential truncated to the fourth order are given.

Quantum sensing with arbitrary frequency resolution

NASA Astrophysics Data System (ADS)

Boss, J. M.; Cujia, K. S.; Zopes, J.; Degen, C. L.

2017-05-01

Quantum sensing takes advantage of well-controlled quantum systems for performing measurements with high sensitivity and precision. We have implemented a concept for quantum sensing with arbitrary frequency resolution, independent of the qubit probe and limited only by the stability of an external synchronization clock. Our concept makes use of quantum lock-in detection to continuously probe a signal of interest. Using the electronic spin of a single nitrogen-vacancy center in diamond, we demonstrate detection of oscillating magnetic fields with a frequency resolution of 70 microhertz over a megahertz bandwidth. The continuous sampling further guarantees an enhanced sensitivity, reaching a signal-to-noise ratio in excess of 104 for a 170-nanotesla test signal measured during a 1-hour interval. Our technique has applications in magnetic resonance spectroscopy, quantum simulation, and sensitive signal detection.

Synthesis of Arbitrary Quantum Circuits to Topological Assembly: Systematic, Online and Compact.

PubMed

Paler, Alexandru; Fowler, Austin G; Wille, Robert

2017-09-05

It is challenging to transform an arbitrary quantum circuit into a form protected by surface code quantum error correcting codes (a variant of topological quantum error correction), especially if the goal is to minimise overhead. One of the issues is the efficient placement of magic state distillation sub circuits, so-called distillation boxes, in the space-time volume that abstracts the computation's required resources. This work presents a general, systematic, online method for the synthesis of such circuits. Distillation box placement is controlled by so-called schedulers. The work introduces a greedy scheduler generating compact box placements. The implemented software, whose source code is available at www.github.com/alexandrupaler/tqec, is used to illustrate and discuss synthesis examples. Synthesis and optimisation improvements are proposed.

Noninvasive measurement of dynamic correlation functions

NASA Astrophysics Data System (ADS)

Uhrich, Philipp; Castrignano, Salvatore; Uys, Hermann; Kastner, Michael

2017-08-01

The measurement of dynamic correlation functions of quantum systems is complicated by measurement backaction. To facilitate such measurements we introduce a protocol, based on weak ancilla-system couplings, that is applicable to arbitrary (pseudo)spin systems and arbitrary equilibrium or nonequilibrium initial states. Different choices of the coupling operator give access to the real and imaginary parts of the dynamic correlation function. This protocol reduces disturbances due to the early-time measurements to a minimum, and we quantify the deviation of the measured correlation functions from the theoretical, unitarily evolved ones. Implementations of the protocol in trapped ions and other experimental platforms are discussed. For spin-1 /2 models and single-site observables we prove that measurement backaction can be avoided altogether, allowing for the use of ancilla-free protocols.

Gradient Pre-Emphasis to Counteract First-Order Concomitant Fields on Asymmetric MRI Gradient Systems

PubMed Central

Tao, Shengzhen; Weavers, Paul T.; Trzasko, Joshua D.; Shu, Yunhong; Huston, John; Lee, Seung-Kyun; Frigo, Louis M.; Bernstein, Matt A.

2016-01-01

PURPOSE To develop a gradient pre-emphasis scheme that prospectively counteracts the effects of the first-order concomitant fields for any arbitrary gradient waveform played on asymmetric gradient systems, and to demonstrate the effectiveness of this approach using a real-time implementation on a compact gradient system. METHODS After reviewing the first-order concomitant fields that are present on asymmetric gradients, a generalized gradient pre-emphasis model assuming arbitrary gradient waveforms is developed to counteract their effects. A numerically straightforward, simple to implement approximate solution to this pre-emphasis problem is derived, which is compatible with the current hardware infrastructure used on conventional MRI scanners for eddy current compensation. The proposed method was implemented on the gradient driver sub-system, and its real-time use was tested using a series of phantom and in vivo data acquired from 2D Cartesian phase-difference, echo-planar imaging (EPI) and spiral acquisitions. RESULTS The phantom and in vivo results demonstrate that unless accounted for, first-order concomitant fields introduce considerable phase estimation error into the measured data and result in images exhibiting spatially dependent blurring/distortion. The resulting artifacts are effectively prevented using the proposed gradient pre-emphasis. CONCLUSION An efficient and effective gradient pre-emphasis framework is developed to counteract the effects of first-order concomitant fields of asymmetric gradient systems. PMID:27373901

Automated Library System Specifications.

DTIC Science & Technology

1986-06-01

University), LIS (Georqetown Universitv Medical Center) 20 DiSTRI3UT!ON.. AVAILABILITY OF ABSTRACT 21 ABSTRACT SECURITY CLASSIFICATION :UNCLASSIFIED...Interface) acquisitions, patron access catalo. (Boolean search), authority Afiles, zana ~ezient reports. Serials control expected in 1985. INDIVIDUALIZATIOI

Laser Beam and Resonator Calculations on Desktop Computers.

NASA Astrophysics Data System (ADS)

Doumont, Jean-Luc

There is a continuing interest in the design and calculation of laser resonators and optical beam propagation. In particular, recently, interest has increased in developing concepts such as one-sided unstable resonators, supergaussian reflectivity profiles, diode laser modes, beam quality concepts, mode competition, excess noise factors, and nonlinear Kerr lenses. To meet these calculation needs, I developed a general-purpose software package named PARAXIA ^{rm TM}, aimed at providing optical scientists and engineers with a set of powerful design and analysis tools that provide rapid and accurate results and are extremely easy to use. PARAXIA can handle separable paraxial optical systems in cartesian or cylindrical coordinates, including complex-valued and misaligned ray matrices, with full diffraction effects between apertures. It includes the following programs:. ABCD provides complex-valued ray-matrix and gaussian -mode analyses for arbitrary paraxial resonators and optical systems, including astigmatism and misalignment in each element. This program required that I generalize the theory of gaussian beam propagation to the case of an off-axis gaussian beam propagating through a misaligned, complex -valued ray matrix. FRESNEL uses FFT and FHT methods to propagate an arbitrary wavefront through an arbitrary paraxial optical system using Huygens' integral in rectangular or radial coordinates. The wavefront can be multiplied by an arbitrary mirror profile and/or saturable gain sheet on each successive propagation through the system. I used FRESNEL to design a one-sided negative-branch unstable resonator for a free -electron laser, and to show how a variable internal aperture influences the mode competition and beam quality in a stable cavity. VSOURCE implements the virtual source analysis to calculate eigenvalues and eigenmodes for unstable resonators with both circular and rectangular hard-edged mirrors (including misaligned rectangular systems). I used VSOURCE to show the validity of the virtual source approach (by comparing its results to those of FRESNEL), to study the properties of hard-edged unstable resonators, and to obtain numerical values of the excess noise factors in such resonators. VRM carries out mode calculations for gaussian variable-reflectivity-mirror lasers. It implements complicated analytical results that I derived to point out the large numerical value of the excess noise factor in geometrically unstable resonators.

Numerical implementation of a cold-ion, Boltzmann-electron model for nonplanar plasma-surface interactions

NASA Astrophysics Data System (ADS)

Holgate, J. T.; Coppins, M.

2018-04-01

Plasma-surface interactions are ubiquitous in the field of plasma science and technology. Much of the physics of these interactions can be captured with a simple model comprising a cold ion fluid and electrons which satisfy the Boltzmann relation. However, this model permits analytical solutions in a very limited number of cases. This paper presents a versatile and robust numerical implementation of the model for arbitrary surface geometries in cartesian and axisymmetric cylindrical coordinates. Specific examples of surfaces with sinusoidal corrugations, trenches, and hemi-ellipsoidal protrusions verify this numerical implementation. The application of the code to problems involving plasma-liquid interactions, plasma etching, and electron emission from the surface is discussed.

Multidimensional NMR inversion without Kronecker products: Multilinear inversion

NASA Astrophysics Data System (ADS)

Medellín, David; Ravi, Vivek R.; Torres-Verdín, Carlos

2016-08-01

Multidimensional NMR inversion using Kronecker products poses several challenges. First, kernel compression is only possible when the kernel matrices are separable, and in recent years, there has been an increasing interest in NMR sequences with non-separable kernels. Second, in three or more dimensions, the singular value decomposition is not unique; therefore kernel compression is not well-defined for higher dimensions. Without kernel compression, the Kronecker product yields matrices that require large amounts of memory, making the inversion intractable for personal computers. Finally, incorporating arbitrary regularization terms is not possible using the Lawson-Hanson (LH) or the Butler-Reeds-Dawson (BRD) algorithms. We develop a minimization-based inversion method that circumvents the above problems by using multilinear forms to perform multidimensional NMR inversion without using kernel compression or Kronecker products. The new method is memory efficient, requiring less than 0.1% of the memory required by the LH or BRD methods. It can also be extended to arbitrary dimensions and adapted to include non-separable kernels, linear constraints, and arbitrary regularization terms. Additionally, it is easy to implement because only a cost function and its first derivative are required to perform the inversion.

Robust computation of dipole electromagnetic fields in arbitrarily anisotropic, planar-stratified environments.

PubMed

Sainath, Kamalesh; Teixeira, Fernando L; Donderici, Burkay

2014-01-01

We develop a general-purpose formulation, based on two-dimensional spectral integrals, for computing electromagnetic fields produced by arbitrarily oriented dipoles in planar-stratified environments, where each layer may exhibit arbitrary and independent anisotropy in both its (complex) permittivity and permeability tensors. Among the salient features of our formulation are (i) computation of eigenmodes (characteristic plane waves) supported in arbitrarily anisotropic media in a numerically robust fashion, (ii) implementation of an hp-adaptive refinement for the numerical integration to evaluate the radiation and weakly evanescent spectra contributions, and (iii) development of an adaptive extension of an integral convergence acceleration technique to compute the strongly evanescent spectrum contribution. While other semianalytic techniques exist to solve this problem, none have full applicability to media exhibiting arbitrary double anisotropies in each layer, where one must account for the whole range of possible phenomena (e.g., mode coupling at interfaces and nonreciprocal mode propagation). Brute-force numerical methods can tackle this problem but only at a much higher computational cost. The present formulation provides an efficient and robust technique for field computation in arbitrary planar-stratified environments. We demonstrate the formulation for a number of problems related to geophysical exploration.

Secular dynamics of hierarchical multiple systems composed of nested binaries, with an arbitrary number of bodies and arbitrary hierarchical structure - II. External perturbations: flybys and supernovae

NASA Astrophysics Data System (ADS)

Hamers, Adrian S.

2018-05-01

We extend the formalism of a previous paper to include the effects of flybys and instantaneous perturbations such as supernovae on the long-term secular evolution of hierarchical multiple systems with an arbitrary number of bodies and hierarchy, provided that the system is composed of nested binary orbits. To model secular encounters, we expand the Hamiltonian in terms of the ratio of the separation of the perturber with respect to the barycentre of the multiple system, to the separation of the widest orbit. Subsequently, we integrate over the perturber orbit numerically or analytically. We verify our method for secular encounters and illustrate it with an example. Furthermore, we describe a method to compute instantaneous orbital changes to multiple systems, such as asymmetric supernovae and impulsive encounters. The secular code, with implementation of the extensions described in this paper, is publicly available within AMUSE, and we provide a number of simple example scripts to illustrate its usage for secular and impulsive encounters and asymmetric supernovae. The extensions presented in this paper are a next step towards efficiently modelling the evolution of complex multiple systems embedded in star clusters.

Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET

PubMed Central

Androsova, Ganna; del Sol, Antonio

2015-01-01

High-throughput technologies have led to the generation of an increasing amount of data in different areas of biology. Datasets capturing the cell’s response to its intra- and extra-cellular microenvironment allows such data to be incorporated as signed and directed graphs or influence networks. These prior knowledge networks (PKNs) represent our current knowledge of the causality of cellular signal transduction. New signalling data is often examined and interpreted in conjunction with PKNs. However, different biological contexts, such as cell type or disease states, may have distinct variants of signalling pathways, resulting in the misinterpretation of new data. The identification of inconsistencies between measured data and signalling topologies, as well as the training of PKNs using context specific datasets (PKN contextualization), are necessary conditions to construct reliable, predictive models, which are current challenges in the systems biology of cell signalling. Here we present PRUNET, a user-friendly software tool designed to address the contextualization of a PKNs to specific experimental conditions. As the input, the algorithm takes a PKN and the expression profile of two given stable steady states or cellular phenotypes. The PKN is iteratively pruned using an evolutionary algorithm to perform an optimization process. This optimization rests in a match between predicted attractors in a discrete logic model (Boolean) and a Booleanized representation of the phenotypes, within a population of alternative subnetworks that evolves iteratively. We validated the algorithm applying PRUNET to four biological examples and using the resulting contextualized networks to predict missing expression values and to simulate well-characterized perturbations. PRUNET constitutes a tool for the automatic curation of a PKN to make it suitable for describing biological processes under particular experimental conditions. The general applicability of the implemented algorithm makes PRUNET suitable for a variety of biological processes, for instance cellular reprogramming or transitions between healthy and disease states. PMID:26058016

Iterative computation of generalized inverses, with an application to CMG steering laws

NASA Technical Reports Server (NTRS)

Steincamp, J. W.

1971-01-01

A cubically convergent iterative method for computing the generalized inverse of an arbitrary M X N matrix A is developed and a FORTRAN subroutine by which the method was implemented for real matrices on a CDC 3200 is given, with a numerical example to illustrate accuracy. Application to a redundant single-gimbal CMG assembly steering law is discussed.

Quantum state engineering by a coherent superposition of photon subtraction and addition

NASA Astrophysics Data System (ADS)

Lee, Su-Yong; Nha, Hyunchul

2011-10-01

We study a coherent superposition tâ+r↠of field annihilation and creation operator acting on continuous variable systems and propose its application for quantum state engineering. We propose an experimental scheme to implement this elementary coherent operation and discuss its usefulness to produce an arbitrary superposition of number states involving up to two photons.

Detecting Lower Bounds to Quantum Channel Capacities.

PubMed

Macchiavello, Chiara; Sacchi, Massimiliano F

2016-04-08

We propose a method to detect lower bounds to quantum capacities of a noisy quantum communication channel by means of a few measurements. The method is easily implementable and does not require any knowledge about the channel. We test its efficiency by studying its performance for most well-known single-qubit noisy channels and for the generalized Pauli channel in an arbitrary finite dimension.

An Autonomous Flight Safety System

DTIC Science & Technology

2008-11-01

are taken. AFSS can take vehicle navigation data from redundant onboard sensors and make flight termination decisions using software-based rules...implemented on redundant flight processors. By basing these decisions on actual Instantaneous Impact Predictions and by providing for an arbitrary...number of mission rules, it is the contention of the AFSS development team that the decision making process used by Missile Flight Control Officers

Synthesizing Biomolecule-based Boolean Logic Gates

PubMed Central

Miyamoto, Takafumi; Razavi, Shiva; DeRose, Robert; Inoue, Takanari

2012-01-01

One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications. PMID:23526588

Interconnect-free parallel logic circuits in a single mechanical resonator

PubMed Central

Mahboob, I.; Flurin, E.; Nishiguchi, K.; Fujiwara, A.; Yamaguchi, H.

2011-01-01

In conventional computers, wiring between transistors is required to enable the execution of Boolean logic functions. This has resulted in processors in which billions of transistors are physically interconnected, which limits integration densities, gives rise to huge power consumption and restricts processing speeds. A method to eliminate wiring amongst transistors by condensing Boolean logic into a single active element is thus highly desirable. Here, we demonstrate a novel logic architecture using only a single electromechanical parametric resonator into which multiple channels of binary information are encoded as mechanical oscillations at different frequencies. The parametric resonator can mix these channels, resulting in new mechanical oscillation states that enable the construction of AND, OR and XOR logic gates as well as multibit logic circuits. Moreover, the mechanical logic gates and circuits can be executed simultaneously, giving rise to the prospect of a parallel logic processor in just a single mechanical resonator. PMID:21326230

Interconnect-free parallel logic circuits in a single mechanical resonator.

PubMed

Mahboob, I; Flurin, E; Nishiguchi, K; Fujiwara, A; Yamaguchi, H

2011-02-15

In conventional computers, wiring between transistors is required to enable the execution of Boolean logic functions. This has resulted in processors in which billions of transistors are physically interconnected, which limits integration densities, gives rise to huge power consumption and restricts processing speeds. A method to eliminate wiring amongst transistors by condensing Boolean logic into a single active element is thus highly desirable. Here, we demonstrate a novel logic architecture using only a single electromechanical parametric resonator into which multiple channels of binary information are encoded as mechanical oscillations at different frequencies. The parametric resonator can mix these channels, resulting in new mechanical oscillation states that enable the construction of AND, OR and XOR logic gates as well as multibit logic circuits. Moreover, the mechanical logic gates and circuits can be executed simultaneously, giving rise to the prospect of a parallel logic processor in just a single mechanical resonator.

Calculating the bidirectional reflectance of natural vegetation covers using Boolean models and geometric optics

NASA Technical Reports Server (NTRS)

Strahler, Alan H.; Li, Xiao-Wen; Jupp, David L. B.

1991-01-01

The bidirectional radiance or reflectance of a forest or woodland can be modeled using principles of geometric optics and Boolean models for random sets in a three dimensional space. This model may be defined at two levels, the scene includes four components; sunlight and shadowed canopy, and sunlit and shadowed background. The reflectance of the scene is modeled as the sum of the reflectances of the individual components as weighted by their areal proportions in the field of view. At the leaf level, the canopy envelope is an assemblage of leaves, and thus the reflectance is a function of the areal proportions of sunlit and shadowed leaf, and sunlit and shadowed background. Because the proportions of scene components are dependent upon the directions of irradiance and exitance, the model accounts for the hotspot that is well known in leaf and tree canopies.

Synthesizing biomolecule-based Boolean logic gates.

PubMed

Miyamoto, Takafumi; Razavi, Shiva; DeRose, Robert; Inoue, Takanari

2013-02-15

One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, and hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.

Satisfiability of logic programming based on radial basis function neural networks

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

Hamadneh, Nawaf; Sathasivam, Saratha; Tilahun, Surafel Luleseged

2014-07-10

In this paper, we propose a new technique to test the Satisfiability of propositional logic programming and quantified Boolean formula problem in radial basis function neural networks. For this purpose, we built radial basis function neural networks to represent the proportional logic which has exactly three variables in each clause. We used the Prey-predator algorithm to calculate the output weights of the neural networks, while the K-means clustering algorithm is used to determine the hidden parameters (the centers and the widths). Mean of the sum squared error function is used to measure the activity of the two algorithms. We appliedmore » the developed technique with the recurrent radial basis function neural networks to represent the quantified Boolean formulas. The new technique can be applied to solve many applications such as electronic circuits and NP-complete problems.« less

Some Applications Of Semigroups And Computer Algebra In Discrete Structures

NASA Astrophysics Data System (ADS)

Bijev, G.

2009-11-01

An algebraic approach to the pseudoinverse generalization problem in Boolean vector spaces is used. A map (p) is defined, which is similar to an orthogonal projection in linear vector spaces. Some other important maps with properties similar to those of the generalized inverses (pseudoinverses) of linear transformations and matrices corresponding to them are also defined and investigated. Let Ax = b be an equation with matrix A and vectors x and b Boolean. Stochastic experiments for solving the equation, which involves the maps defined and use computer algebra methods, have been made. As a result, the Hamming distance between vectors Ax = p(b) and b is equal or close to the least possible. We also share our experience in using computer algebra systems for teaching discrete mathematics and linear algebra and research. Some examples for computations with binary relations using Maple are given.

Altered Micro-RNA Degradation Promotes Tumor Heterogeneity: A Result from Boolean Network Modeling.

PubMed

Wu, Yunyi; Krueger, Gerhard R F; Wang, Guanyu

2016-02-01

Cancer heterogeneity may reflect differential dynamical outcomes of the regulatory network encompassing biomolecules at both transcriptional and post-transcriptional levels. In other words, differential gene-expression profiles may correspond to different stable steady states of a mathematical model for simulation of biomolecular networks. To test this hypothesis, we simplified a regulatory network that is important for soft-tissue sarcoma metastasis and heterogeneity, comprising of transcription factors, micro-RNAs, and signaling components of the NOTCH pathway. We then used a Boolean network model to simulate the dynamics of this network, and particularly investigated the consequences of differential miRNA degradation modes. We found that efficient miRNA degradation is crucial for sustaining a homogenous and healthy phenotype, while defective miRNA degradation may lead to multiple stable steady states and ultimately to carcinogenesis and heterogeneity. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Lattice Theory, Measures and Probability

NASA Astrophysics Data System (ADS)

Knuth, Kevin H.

2007-11-01

In this tutorial, I will discuss the concepts behind generalizing ordering to measuring and apply these ideas to the derivation of probability theory. The fundamental concept is that anything that can be ordered can be measured. Since we are in the business of making statements about the world around us, we focus on ordering logical statements according to implication. This results in a Boolean lattice, which is related to the fact that the corresponding logical operations form a Boolean algebra. The concept of logical implication can be generalized to degrees of implication by generalizing the zeta function of the lattice. The rules of probability theory arise naturally as a set of constraint equations. Through this construction we are able to neatly connect the concepts of order, structure, algebra, and calculus. The meaning of probability is inherited from the meaning of the ordering relation, implication, rather than being imposed in an ad hoc manner at the start.

Polynomial algebra of discrete models in systems biology.

PubMed

Veliz-Cuba, Alan; Jarrah, Abdul Salam; Laubenbacher, Reinhard

2010-07-01

An increasing number of discrete mathematical models are being published in Systems Biology, ranging from Boolean network models to logical models and Petri nets. They are used to model a variety of biochemical networks, such as metabolic networks, gene regulatory networks and signal transduction networks. There is increasing evidence that such models can capture key dynamic features of biological networks and can be used successfully for hypothesis generation. This article provides a unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets. They can be represented as polynomial dynamical systems, which allows the use of a variety of mathematical tools from computer algebra for their analysis. Algorithms are presented for the translation into polynomial dynamical systems. Examples are given of how polynomial algebra can be used for the model analysis. alanavc@vt.edu Supplementary data are available at Bioinformatics online.

Graphene-based non-Boolean logic circuits

NASA Astrophysics Data System (ADS)

Liu, Guanxiong; Ahsan, Sonia; Khitun, Alexander G.; Lake, Roger K.; Balandin, Alexander A.

2013-10-01

Graphene revealed a number of unique properties beneficial for electronics. However, graphene does not have an energy band-gap, which presents a serious hurdle for its applications in digital logic gates. The efforts to induce a band-gap in graphene via quantum confinement or surface functionalization have not resulted in a breakthrough. Here we show that the negative differential resistance experimentally observed in graphene field-effect transistors of "conventional" design allows for construction of viable non-Boolean computational architectures with the gapless graphene. The negative differential resistance—observed under certain biasing schemes—is an intrinsic property of graphene, resulting from its symmetric band structure. Our atomistic modeling shows that the negative differential resistance appears not only in the drift-diffusion regime but also in the ballistic regime at the nanometer-scale—although the physics changes. The obtained results present a conceptual change in graphene research and indicate an alternative route for graphene's applications in information processing.

Generation of arbitrary order Bessel beams via 3D printed axicons at the terahertz frequency range.

PubMed

Wei, Xuli; Liu, Changming; Niu, Liting; Zhang, Zhongqi; Wang, Kejia; Yang, Zhengang; Liu, Jinsong

2015-12-20

We present the generation of arbitrary order Bessel beams at 0.3 THz through the implementation of suitably designed axicons based on 3D printing technology. The helical axicons, which possess thickness gradients in both radial and azimuthal directions, can convert the incident Gaussian beam into a high-order Bessel beam with spiral phase structure. The evolution of the generated Bessel beams are characterized experimentally with a three-dimensional field scanner. Moreover, the topological charges carried by the high-order Bessel beams are determined by the fork-like interferograms. This 3D-printing-based Bessel beam generation technique is useful not only for THz imaging systems with zero-order Bessel beams but also for future orbital-angular-momentum-based THz free-space communication with higher-order Bessel beams.

Quantum state engineering using one-dimensional discrete-time quantum walks

NASA Astrophysics Data System (ADS)

Innocenti, Luca; Majury, Helena; Giordani, Taira; Spagnolo, Nicolò; Sciarrino, Fabio; Paternostro, Mauro; Ferraro, Alessandro

2017-12-01

Quantum state preparation in high-dimensional systems is an essential requirement for many quantum-technology applications. The engineering of an arbitrary quantum state is, however, typically strongly dependent on the experimental platform chosen for implementation, and a general framework is still missing. Here we show that coined quantum walks on a line, which represent a framework general enough to encompass a variety of different platforms, can be used for quantum state engineering of arbitrary superpositions of the walker's sites. We achieve this goal by identifying a set of conditions that fully characterize the reachable states in the space comprising walker and coin and providing a method to efficiently compute the corresponding set of coin parameters. We assess the feasibility of our proposal by identifying a linear optics experiment based on photonic orbital angular momentum technology.

A Walking Method for Non-Decomposition Intersection and Union of Arbitrary Polygons and Polyhedrons

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

Graham, M.; Yao, J.

We present a method for computing the intersection and union of non- convex polyhedrons without decomposition in O(n log n) time, where n is the total number of faces of both polyhedrons. We include an accompanying Python package which addresses many of the practical issues associated with implementation and serves as a proof of concept. The key to the method is that by considering the edges of the original ob- jects and the intersections between faces as walking routes, we can e ciently nd the boundary of the intersection of arbitrary objects using directional walks, thus handling the concave casemore » in a natural manner. The method also easily extends to plane slicing and non-convex polyhedron unions, and both the polyhedron and its constituent faces may be non-convex.« less

Cross-vendor evaluation of key user-defined clinical decision support capabilities: a scenario-based assessment of certified electronic health records with guidelines for future development

PubMed Central

Wright, Adam; Sittig, Dean F

2015-01-01

Objective Clinical decision support (CDS) is essential for delivery of high-quality, cost-effective, and safe healthcare. The authors sought to evaluate the CDS capabilities across electronic health record (EHR) systems. Methods We evaluated the CDS implementation capabilities of 8 Office of the National Coordinator for Health Information Technology Authorized Certification Body (ONC-ACB)-certified EHRs. Within each EHR, the authors attempted to implement 3 user-defined rules that utilized the various data and logic elements expected of typical EHRs and that represented clinically important evidenced-based care. The rules were: 1) if a patient has amiodarone on his or her active medication list and does not have a thyroid-stimulating hormone (TSH) result recorded in the last 12 months, suggest ordering a TSH; 2) if a patient has a hemoglobin A1c result >7% and does not have diabetes on his or her problem list, suggest adding diabetes to the problem list; and 3) if a patient has coronary artery disease on his or her problem list and does not have aspirin on the active medication list, suggest ordering aspirin. Results Most evaluated EHRs lacked some CDS capabilities; 5 EHRs were able to implement all 3 rules, and the remaining 3 EHRs were unable to implement any of the rules. One of these did not allow users to customize CDS rules at all. The most frequently found shortcomings included the inability to use laboratory test results in rules, limit rules by time, use advanced Boolean logic, perform actions from the alert interface, and adequately test rules. Conclusion Significant improvements in the EHR certification and implementation procedures are necessary. PMID:26104739

Factors associated with sustained remission in patients with rheumatoid arthritis.

PubMed

Martire, María Victoria; Marino Claverie, Lucila; Duarte, Vanesa; Secco, Anastasia; Mammani, Marta

2015-01-01

To find out the factors that are associated with sustained remission measured by DAS28 and boolean ACR EULAR 2011 criteria at the time of diagnosis of rheumatoid arthritis. Medical records of patients with rheumatoid arthritis in sustained remission according to DAS28 were reviewed. They were compared with patients who did not achieved values of DAS28<2.6 in any visit during the first 3 years after diagnosis. We also evaluated if patients achieved the boolean ACR/EULAR criteria. Variables analyzed: sex, age, smoking, comorbidities, rheumatoid factor, anti-CCP, ESR, CRP, erosions, HAQ, DAS28, extra-articular manifestations, time to initiation of treatment, involvement of large joints, number of tender joints, number of swollen joints, pharmacological treatment. Forty five patients that achieved sustained remission were compared with 44 controls. The variables present at diagnosis that significantly were associated with remission by DAS28 were: lower values of DAS28, HAQ, ESR, NTJ, NSJ, negative CRP, absence of erosions, male sex and absence of involvement of large joints. Only 24.71% achieved the boolean criteria. The variables associated with sustained remission by these criteria were: lower values of DAS28, HAQ, ESR, number of tender joints and number of swollen joints, negative CRP and absence of erosions. The factors associated with sustained remission were the lower baseline disease activity, the low degree of functional disability and lower joint involvement. We consider it important to recognize these factors to optimize treatment. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

Boolean Operations with Prism Algebraic Patches

PubMed Central

Bajaj, Chandrajit; Paoluzzi, Alberto; Portuesi, Simone; Lei, Na; Zhao, Wenqi

2009-01-01

In this paper we discuss a symbolic-numeric algorithm for Boolean operations, closed in the algebra of curved polyhedra whose boundary is triangulated with algebraic patches (A-patches). This approach uses a linear polyhedron as a first approximation of both the arguments and the result. On each triangle of a boundary representation of such linear approximation, a piecewise cubic algebraic interpolant is built, using a C1-continuous prism algebraic patch (prism A-patch) that interpolates the three triangle vertices, with given normal vectors. The boundary representation only stores the vertices of the initial triangulation and their external vertex normals. In order to represent also flat and/or sharp local features, the corresponding normal-per-face and/or normal-per-edge may be also given, respectively. The topology is described by storing, for each curved triangle, the two triples of pointers to incident vertices and to adjacent triangles. For each triangle, a scaffolding prism is built, produced by its extreme vertices and normals, which provides a containment volume for the curved interpolating A-patch. When looking for the result of a regularized Boolean operation, the 0-set of a tri-variate polynomial within each such prism is generated, and intersected with the analogous 0-sets of the other curved polyhedron, when two prisms have non-empty intersection. The intersection curves of the boundaries are traced and used to decompose each boundary into the 3 standard classes of subpatches, denoted in, out and on. While tracing the intersection curves, the locally refined triangulation of intersecting patches is produced, and added to the boundary representation. PMID:21516262

Computing smallest intervention strategies for multiple metabolic networks in a boolean model.

PubMed

Lu, Wei; Tamura, Takeyuki; Song, Jiangning; Akutsu, Tatsuya

2015-02-01

This article considers the problem whereby, given two metabolic networks N1 and N2, a set of source compounds, and a set of target compounds, we must find the minimum set of reactions whose removal (knockout) ensures that the target compounds are not producible in N1 but are producible in N2. Similar studies exist for the problem of finding the minimum knockout with the smallest side effect for a single network. However, if technologies of external perturbations are advanced in the near future, it may be important to develop methods of computing the minimum knockout for multiple networks (MKMN). Flux balance analysis (FBA) is efficient if a well-polished model is available. However, that is not always the case. Therefore, in this article, we study MKMN in Boolean models and an elementary mode (EM)-based model. Integer linear programming (ILP)-based methods are developed for these models, since MKMN is NP-complete for both the Boolean model and the EM-based model. Computer experiments are conducted with metabolic networks of clostridium perfringens SM101 and bifidobacterium longum DJO10A, respectively known as bad bacteria and good bacteria for the human intestine. The results show that larger networks are more likely to have MKMN solutions. However, solving for these larger networks takes a very long time, and often the computation cannot be completed. This is reasonable, because small networks do not have many alternative pathways, making it difficult to satisfy the MKMN condition, whereas in large networks the number of candidate solutions explodes. Our developed software minFvskO is available online.

THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

The new THttpServer class in ROOT implements HTTP server for arbitrary ROOT applications. It is based on Civetweb embeddable HTTP server and provides direct access to all objects registered for the server. Objects data could be provided in different formats: binary, XML, GIF/PNG, and JSON. A generic user interface for THttpServer has been implemented with HTML/JavaScript based on JavaScript ROOT development. With any modern web browser one could list, display, and monitor objects available on the server. THttpServer is used in Go4 framework to provide HTTP interface to the online analysis.

Modified signed-digit arithmetic based on redundant bit representation.

PubMed

Huang, H; Itoh, M; Yatagai, T

1994-09-10

Fully parallel modified signed-digit arithmetic operations are realized based on redundant bit representation of the digits proposed. A new truth-table minimizing technique is presented based on redundant-bitrepresentation coding. It is shown that only 34 minterms are enough for implementing one-step modified signed-digit addition and subtraction with this new representation. Two optical implementation schemes, correlation and matrix multiplication, are described. Experimental demonstrations of the correlation architecture are presented. Both architectures use fixed minterm masks for arbitrary-length operands, taking full advantage of the parallelism of the modified signed-digit number system and optics.

Cluster-state quantum computing enhanced by high-fidelity generalized measurements.

PubMed

Biggerstaff, D N; Kaltenbaek, R; Hamel, D R; Weihs, G; Rudolph, T; Resch, K J

2009-12-11

We introduce and implement a technique to extend the quantum computational power of cluster states by replacing some projective measurements with generalized quantum measurements (POVMs). As an experimental demonstration we fully realize an arbitrary three-qubit cluster computation by implementing a tunable linear-optical POVM, as well as fast active feedforward, on a two-qubit photonic cluster state. Over 206 different computations, the average output fidelity is 0.9832+/-0.0002; furthermore the error contribution from our POVM device and feedforward is only of O(10(-3)), less than some recent thresholds for fault-tolerant cluster computing.

Configurable unitary transformations and linear logic gates using quantum memories.

PubMed

Campbell, G T; Pinel, O; Hosseini, M; Ralph, T C; Buchler, B C; Lam, P K

2014-08-08

We show that a set of optical memories can act as a configurable linear optical network operating on frequency-multiplexed optical states. Our protocol is applicable to any quantum memories that employ off-resonant Raman transitions to store optical information in atomic spins. In addition to the configurability, the protocol also offers favorable scaling with an increasing number of modes where N memories can be configured to implement arbitrary N-mode unitary operations during storage and readout. We demonstrate the versatility of this protocol by showing an example where cascaded memories are used to implement a conditional cz gate.

A Note about Information Science Research.

ERIC Educational Resources Information Center

Salton, Gerard

1985-01-01

Discusses the relationship between information science research and practice and briefly describes current research on 10 topics in information retrieval literature: vector processing retrieval strategy, probabilistic retrieval models, inverted file procedures, relevance feedback, Boolean query formulations, front-end procedures, citation…

Bibliographic Instruction in the 21st Century.

ERIC Educational Resources Information Center

Poirier, Gayle

2000-01-01

Discusses bibliographic instruction in libraries. Topics include a history of bibliographic instruction; the Internet and electronic searching; librarians' use of technology; defining information needs; locating and accessing information, including classification systems and Boolean searching; evaluating information; using and communication…

"Visions" for Children's Health and Wellbeing: Exploring the Complex and Arbitrary Processes of Putting Theory into Practice

ERIC Educational Resources Information Center

Wellard, Ian; Secker, Michelle

2017-01-01

It could be claimed that the priority of any Government should be to look after the interests of the public it serves. Much of this role includes attempting to actively develop and implement policies and programmes that best contribute to or enhance general standards of living. Addressing health and wellbeing, it follows, is a reasonable vision…

Reducing full one-loop amplitudes to scalar integrals at the integrand level

NASA Astrophysics Data System (ADS)

Ossola, Giovanni; Papadopoulos, Costas G.; Pittau, Roberto

2007-02-01

We show how to extract the coefficients of the 4-, 3-, 2- and 1-point one-loop scalar integrals from the full one-loop amplitude of arbitrary scattering processes. In a similar fashion, also the rational terms can be derived. Basically no information on the analytical structure of the amplitude is required, making our method appealing for an efficient numerical implementation.

A simple finite element method for linear hyperbolic problems

DOE PAGES

Mu, Lin; Ye, Xiu

2017-09-14

Here, we introduce a simple finite element method for solving first order hyperbolic equations with easy implementation and analysis. Our new method, with a symmetric, positive definite system, is designed to use discontinuous approximations on finite element partitions consisting of arbitrary shape of polygons/polyhedra. Error estimate is established. Extensive numerical examples are tested that demonstrate the robustness and flexibility of the method.

A simple finite element method for linear hyperbolic problems

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

Mu, Lin; Ye, Xiu

Here, we introduce a simple finite element method for solving first order hyperbolic equations with easy implementation and analysis. Our new method, with a symmetric, positive definite system, is designed to use discontinuous approximations on finite element partitions consisting of arbitrary shape of polygons/polyhedra. Error estimate is established. Extensive numerical examples are tested that demonstrate the robustness and flexibility of the method.

Exploitation of Unintentional Information Leakage from Integrated Circuits

DTIC Science & Technology

2011-12-01

U.S. Defense Science Board Task Force examined the effects and risks of outsourcing high performance microchip production to foreign countries [Off05...mapping methodology is developed and demon- strated to comprehensively assess the information leakage of arbitrary block cipher implementations. The...engineering poses a serious threat since it can en- able competitors or adversaries to bypass years of research and development through counterfeiting or

Gradient pre-emphasis to counteract first-order concomitant fields on asymmetric MRI gradient systems.

PubMed

Tao, Shengzhen; Weavers, Paul T; Trzasko, Joshua D; Shu, Yunhong; Huston, John; Lee, Seung-Kyun; Frigo, Louis M; Bernstein, Matt A

2017-06-01

To develop a gradient pre-emphasis scheme that prospectively counteracts the effects of the first-order concomitant fields for any arbitrary gradient waveform played on asymmetric gradient systems, and to demonstrate the effectiveness of this approach using a real-time implementation on a compact gradient system. After reviewing the first-order concomitant fields that are present on asymmetric gradients, we developed a generalized gradient pre-emphasis model assuming arbitrary gradient waveforms to counteract their effects. A numerically straightforward, easily implemented approximate solution to this pre-emphasis problem was derived that was compatible with the current hardware infrastructure of conventional MRI scanners for eddy current compensation. The proposed method was implemented on the gradient driver subsystem, and its real-time use was tested using a series of phantom and in vivo data acquired from two-dimensional Cartesian phase-difference, echo-planar imaging, and spiral acquisitions. The phantom and in vivo results demonstrated that unless accounted for, first-order concomitant fields introduce considerable phase estimation error into the measured data and result in images with spatially dependent blurring/distortion. The resulting artifacts were effectively prevented using the proposed gradient pre-emphasis. We have developed an efficient and effective gradient pre-emphasis framework to counteract the effects of first-order concomitant fields of asymmetric gradient systems. Magn Reson Med 77:2250-2262, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Formal specification and mechanical verification of SIFT - A fault-tolerant flight control system

NASA Technical Reports Server (NTRS)

Melliar-Smith, P. M.; Schwartz, R. L.

1982-01-01

The paper describes the methodology being employed to demonstrate rigorously that the SIFT (software-implemented fault-tolerant) computer meets its requirements. The methodology uses a hierarchy of design specifications, expressed in the mathematical domain of multisorted first-order predicate calculus. The most abstract of these, from which almost all details of mechanization have been removed, represents the requirements on the system for reliability and intended functionality. Successive specifications in the hierarchy add design and implementation detail until the PASCAL programs implementing the SIFT executive are reached. A formal proof that a SIFT system in a 'safe' state operates correctly despite the presence of arbitrary faults has been completed all the way from the most abstract specifications to the PASCAL program.

Environment dependent enhanced photoluminescence and Boolean logic gates like behavior of Bi2O3 and Ag:Bi2O3 nanostructures

NASA Astrophysics Data System (ADS)

Hariharan, S.; Karthikeyan, B.

2018-03-01

In the evolution of nanotechnology research for smart and precise sensor fabrication, here we report the implementation of simple logic gate operations performing by luminescent nanostructures in biomolecule environment based on photoluminescence (PL) technique. This present work deals with the luminescence property of α-Bi2O3 and Ag modified α-Bi2O3 nanostructures for D-glucose and Bovine serum albumin (BSA) sensing applications. These nanostructures are prepared by simple co-precipitation method and their morphology are examined using transmission electron microscope (TEM). We explore the PL characteristics of the prepared nanostructures and observe their change in PL intensity in the presence of D-glucose and BSA molecules. Enhancement in PL intensity is observed in the presence of D-glucose and BSA. Based on the PL response of prepared nanostructures in the biomolecule environment, we demonstrate biophotonic logic gates including YES, PASS 0, OR and INHIBIT gates.

Clean Quantum and Classical Communication Protocols.

PubMed

Buhrman, Harry; Christandl, Matthias; Perry, Christopher; Zuiddam, Jeroen

2016-12-02

By how much must the communication complexity of a function increase if we demand that the parties not only correctly compute the function but also return all registers (other than the one containing the answer) to their initial states at the end of the communication protocol? Protocols that achieve this are referred to as clean and the associated cost as the clean communication complexity. Here we present clean protocols for calculating the inner product of two n-bit strings, showing that (in the absence of preshared entanglement) at most n+3 qubits or n+O(sqrt[n]) bits of communication are required. The quantum protocol provides inspiration for obtaining the optimal method to implement distributed cnot gates in parallel while minimizing the amount of quantum communication. For more general functions, we show that nearly all Boolean functions require close to 2n bits of classical communication to compute and close to n qubits if the parties have access to preshared entanglement. Both of these values are maximal for their respective paradigms.

Simulation of all-optical logic NOR gate based on two-photon absorption with semiconductor optical amplifier-assisted Mach-Zehnder interferometer with the effect of amplified spontaneous emission

NASA Astrophysics Data System (ADS)

Kotb, Amer

2015-05-01

The performance of an all-optical NOR gate is numerically simulated and investigated. The NOR Boolean function is realized by using a semiconductor optical amplifier (SOA) incorporated in Mach-Zehnder interferometer (MZI) arms and exploiting the nonlinear effect of two-photon absorption (TPA). If the input pulse intensities is adjusting to be high enough, the TPA-induced phase change can be larger than the regular gain-induced phase change and hence support ultrafast operation in the dual rail switching mode. The numerical study is carried out by taking into account the effect of the amplified spontaneous emission (ASE). The dependence of the output quality factor ( Q-factor) on critical data signals and SOAs parameters is examined and assessed. The obtained results confirm that the NOR gate implemented with the proposed scheme is capable of operating at a data rate of 250 Gb/s with logical correctness and high output Q-factor.

Quantum Vertex Model for Reversible Classical Computing

NASA Astrophysics Data System (ADS)

Chamon, Claudio; Mucciolo, Eduardo; Ruckenstein, Andrei; Yang, Zhicheng

We present a planar vertex model that encodes the result of a universal reversible classical computation in its ground state. The approach involves Boolean variables (spins) placed on links of a two-dimensional lattice, with vertices representing logic gates. Large short-ranged interactions between at most two spins implement the operation of each gate. The lattice is anisotropic with one direction corresponding to computational time, and with transverse boundaries storing the computation's input and output. The model displays no finite temperature phase transitions, including no glass transitions, independent of circuit. The computational complexity is encoded in the scaling of the relaxation rate into the ground state with the system size. We use thermal annealing and a novel and more efficient heuristic \\x9Dannealing with learning to study various computational problems. To explore faster relaxation routes, we construct an explicit mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating a novel approach to reversible classical computation based on quantum annealing.

Extremal Optimization for Quadratic Unconstrained Binary Problems

NASA Astrophysics Data System (ADS)

Boettcher, S.

We present an implementation of τ-EO for quadratic unconstrained binary optimization (QUBO) problems. To this end, we transform modify QUBO from its conventional Boolean presentation into a spin glass with a random external field on each site. These fields tend to be rather large compared to the typical coupling, presenting EO with a challenging two-scale problem, exploring smaller differences in couplings effectively while sufficiently aligning with those strong external fields. However, we also find a simple solution to that problem that indicates that those external fields apparently tilt the energy landscape to a such a degree such that global minima become more easy to find than those of spin glasses without (or very small) fields. We explore the impact of the weight distribution of the QUBO formulation in the operations research literature and analyze their meaning in a spin-glass language. This is significant because QUBO problems are considered among the main contenders for NP-hard problems that could be solved efficiently on a quantum computer such as D-Wave.

A.I.-based real-time support for high performance aircraft operations

NASA Technical Reports Server (NTRS)

Vidal, J. J.

1985-01-01

Artificial intelligence (AI) based software and hardware concepts are applied to the handling system malfunctions during flight tests. A representation of malfunction procedure logic using Boolean normal forms are presented. The representation facilitates the automation of malfunction procedures and provides easy testing for the embedded rules. It also forms a potential basis for a parallel implementation in logic hardware. The extraction of logic control rules, from dynamic simulation and their adaptive revision after partial failure are examined. It uses a simplified 2-dimensional aircraft model with a controller that adaptively extracts control rules for directional thrust that satisfies a navigational goal without exceeding pre-established position and velocity limits. Failure recovery (rule adjusting) is examined after partial actuator failure. While this experiment was performed with primitive aircraft and mission models, it illustrates an important paradigm and provided complexity extrapolations for the proposed extraction of expertise from simulation, as discussed. The use of relaxation and inexact reasoning in expert systems was also investigated.

Integrating Query of Relational and Textual Data in Clinical Databases: A Case Study

PubMed Central

Fisk, John M.; Mutalik, Pradeep; Levin, Forrest W.; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

2003-01-01

Objectives: The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Design: Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Measurements: Results are relevance-ranked using either “total documents per patient” or “report type weighting.” Results: Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. Conclusion: A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers. PMID:12509355

A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN)

NASA Astrophysics Data System (ADS)

Hernández-Hernández, Valeria; Barrio, Rafael A.; Benítez, Mariana; Nakayama, Naomi; Romero-Arias, José Roberto; Villarreal, Carlos

2018-05-01

Intracellular polarisation of auxin efflux carriers is crucial for understanding how auxin gradients form in plants. The polarisation dynamics of auxin efflux carriers PIN-FORMED (PIN) depends on both biomechanical forces as well as chemical, molecular and genetic factors. Biomechanical forces have shown to affect the localisation of PIN transporters to the plasma membrane. We propose a physico-genetic module of PIN polarisation that integrates biomechanical, molecular, and cellular processes as well as their non-linear interactions. The module was implemented as a discrete Boolean model and then approximated to a continuous dynamic system, in order to explore the relative contribution of the factors mediating PIN polarisation at the scale of single cell. Our models recovered qualitative behaviours that have been experimentally observed and enable us to predict that, in the context of PIN polarisation, the effects of the mechanical forces can predominate over the activity of molecular factors such as the GTPase ROP6 and the ROP-INTERACTIVE CRIB MOTIF-CONTAINING PROTEIN RIC1.

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.

TemperSAT: A new efficient fair-sampling random k-SAT solver

NASA Astrophysics Data System (ADS)

Fang, Chao; Zhu, Zheng; Katzgraber, Helmut G.

The set membership problem is of great importance to many applications and, in particular, database searches for target groups. Recently, an approach to speed up set membership searches based on the NP-hard constraint-satisfaction problem (random k-SAT) has been developed. However, the bottleneck of the approach lies in finding the solution to a large SAT formula efficiently and, in particular, a large number of independent solutions is needed to reduce the probability of false positives. Unfortunately, traditional random k-SAT solvers such as WalkSAT are biased when seeking solutions to the Boolean formulas. By porting parallel tempering Monte Carlo to the sampling of binary optimization problems, we introduce a new algorithm (TemperSAT) whose performance is comparable to current state-of-the-art SAT solvers for large k with the added benefit that theoretically it can find many independent solutions quickly. We illustrate our results by comparing to the currently fastest implementation of WalkSAT, WalkSATlm.

Designed Transcriptional Regulation in Mammalian Cells Based on TALE- and CRISPR/dCas9.

PubMed

Lebar, Tina; Jerala, Roman

2018-01-01

Transcriptional regulation lies at the center of many cellular processes and is the result of cellular response to different external and internal signals. Control of transcription of selected genes enables an unprecedented access to shape the cellular response. While orthogonal transcription factors from bacteria, yeast, plants, or other cells have been used to introduce new cellular logic into mammalian cells, the discovery of designable modular DNA binding domains, such as Transcription Activator-Like Effectors (TALEs) and the CRISPR system, enable targeting of almost any selected DNA sequence. Fusion or conditional association of DNA targeting domain with transcriptional effector domains enables controlled regulation of almost any endogenous or ectopic gene. Moreover, the designed regulators can be linked into genetic circuits to implement complex responses, such as different types of Boolean functions and switches. In this chapter, we describe the protocols for achieving efficient transcriptional regulation with TALE- and CRISPR-based designed transcription factors in mammalian cells.

Integrating causal reasoning at different levels of abstraction. [in problem-solving system functioning as pilot assistant in commercial air transport emergencies

NASA Technical Reports Server (NTRS)

Hudlicka, Eva; Corker, Kevin

1988-01-01

In this paper, a problem-solving system which uses a multilevel causal model of its domain is described. The system functions in the role of a pilot's assistant in the domain of commercial air transport emergencies. The model represents causal relationships among the aircraft subsystems, the effectors (engines, control surfaces), the forces that act on an aircraft in flight (thrust, lift), and the aircraft's flight profile (speed, altitude, etc.). The causal relationships are represented at three levels of abstraction: Boolean, qualitative, and quantitative, and reasoning about causes and effects can take place at each of these levels. Since processing at each level has different characteristics with respect to speed, the type of data required, and the specificity of the results, the problem-solving system can adapt to a wide variety of situations. The system is currently being implemented in the KEE(TM) development environment on a Symbolics Lisp machine.

Carrots and sticks: compliance provisions in state competitive food laws-examples for state and local implementation of the updated USDA standards.

PubMed

Gourdet, Camille K; Chriqui, Jamie F; Piekarz, Elizabeth; Dang, Quang; Chaloupka, Frank J

2014-07-01

Competitive foods remain prevalent in schools even though the majority of states' laws have addressed this for several years. Whereas updated federal standards take effect during school year 2014-2015, aspects of competitive food regulation will remain relegated to the states and districts and concerns exist about compliance with the federal standards. This study examined compliance provisions codified into state law that focused on incentives, monetary penalties, or contracts which could provide examples for other jurisdictions. Codified statutory and administrative laws effective as of January 2013 for all 50 states and the District of Columbia were compiled using Boolean searches in Lexis-Nexis and Westlaw. All laws were analyzed by 2 study authors to determine the presence and components of relevant provisions. Eighteen states' laws contained compliance mechanisms including financial and/or programmatic incentives (5 states), contract provisions (11 states), and monetary penalties for noncompliance (7 states). Five states' laws contained a combination of approaches. Compliance measures help to strengthen competitive food laws by providing state agencies with an enforcement mechanism. Enforcing such provisions will help to create healthier school environments. This study will provide useful insight for governments at all levels as they implement competitive food laws. © 2014, American School Health Association.

A fungicide-responsive kinase as a tool for synthetic cell fate regulation.

PubMed

Furukawa, Kentaro; Hohmann, Stefan

2015-08-18

Engineered biological systems that precisely execute defined tasks have major potential for medicine and biotechnology. For instance, gene- or cell-based therapies targeting pathogenic cells may replace time- and resource-intensive drug development. Engineering signal transduction systems is a promising, yet presently underexplored approach. Here, we exploit a fungicide-responsive heterologous histidine kinase for pathway engineering and synthetic cell fate regulation in the budding yeast Saccharomyces cerevisiae. Rewiring the osmoregulatory Hog1 MAPK signalling system generates yeast cells programmed to execute three different tasks. First, a synthetic negative feedback loop implemented by employing the fungicide-responsive kinase and a fungicide-resistant derivative reshapes the Hog1 activation profile, demonstrating how signalling dynamics can be engineered. Second, combinatorial integration of different genetic parts including the histidine kinases, a pathway activator and chemically regulated promoters enables control of yeast growth and/or gene expression in a two-input Boolean logic manner. Finally, we implemented a genetic 'suicide attack' system, in which engineered cells eliminate target cells and themselves in a specific and controllable manner. Taken together, fungicide-responsive kinases can be applied in different constellations to engineer signalling behaviour. Sensitizing engineered cells to existing chemicals may be generally useful for future medical and biotechnological applications. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multi-scale graph-cut algorithm for efficient water-fat separation.

PubMed

Berglund, Johan; Skorpil, Mikael

2017-09-01

To improve the accuracy and robustness to noise in water-fat separation by unifying the multiscale and graph cut based approaches to B 0 -correction. A previously proposed water-fat separation algorithm that corrects for B 0 field inhomogeneity in 3D by a single quadratic pseudo-Boolean optimization (QPBO) graph cut was incorporated into a multi-scale framework, where field map solutions are propagated from coarse to fine scales for voxels that are not resolved by the graph cut. The accuracy of the single-scale and multi-scale QPBO algorithms was evaluated against benchmark reference datasets. The robustness to noise was evaluated by adding noise to the input data prior to water-fat separation. Both algorithms achieved the highest accuracy when compared with seven previously published methods, while computation times were acceptable for implementation in clinical routine. The multi-scale algorithm was more robust to noise than the single-scale algorithm, while causing only a small increase (+10%) of the reconstruction time. The proposed 3D multi-scale QPBO algorithm offers accurate water-fat separation, robustness to noise, and fast reconstruction. The software implementation is freely available to the research community. Magn Reson Med 78:941-949, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Terahertz bandwidth all-optical Hilbert transformers based on long-period gratings.

PubMed

Ashrafi, Reza; Azaña, José

2012-07-01

A novel, all-optical design for implementing terahertz (THz) bandwidth real-time Hilbert transformers is proposed and numerically demonstrated. An all-optical Hilbert transformer can be implemented using a uniform-period long-period grating (LPG) with a properly designed amplitude-only grating apodization profile, incorporating a single π-phase shift in the middle of the grating length. The designed LPG-based Hilbert transformers can be practically implemented using either fiber-optic or integrated-waveguide technologies. As a generalization, photonic fractional Hilbert transformers are also designed based on the same optical platform. In this general case, the resulting LPGs have multiple π-phase shifts along the grating length. Our numerical simulations confirm that all-optical Hilbert transformers capable of processing arbitrary optical signals with bandwidths well in the THz range can be implemented using feasible fiber/waveguide LPG designs.

Microseismic Full Waveform Modeling in Anisotropic Media with Moment Tensor Implementation

NASA Astrophysics Data System (ADS)

Shi, Peidong; Angus, Doug; Nowacki, Andy; Yuan, Sanyi; Wang, Yanyan

2018-03-01

Seismic anisotropy which is common in shale and fractured rocks will cause travel-time and amplitude discrepancy in different propagation directions. For microseismic monitoring which is often implemented in shale or fractured rocks, seismic anisotropy needs to be carefully accounted for in source location and mechanism determination. We have developed an efficient finite-difference full waveform modeling tool with an arbitrary moment tensor source. The modeling tool is suitable for simulating wave propagation in anisotropic media for microseismic monitoring. As both dislocation and non-double-couple source are often observed in microseismic monitoring, an arbitrary moment tensor source is implemented in our forward modeling tool. The increments of shear stress are equally distributed on the staggered grid to implement an accurate and symmetric moment tensor source. Our modeling tool provides an efficient way to obtain the Green's function in anisotropic media, which is the key of anisotropic moment tensor inversion and source mechanism characterization in microseismic monitoring. In our research, wavefields in anisotropic media have been carefully simulated and analyzed in both surface array and downhole array. The variation characteristics of travel-time and amplitude of direct P- and S-wave in vertical transverse isotropic media and horizontal transverse isotropic media are distinct, thus providing a feasible way to distinguish and identify the anisotropic type of the subsurface. Analyzing the travel-times and amplitudes of the microseismic data is a feasible way to estimate the orientation and density of the induced cracks in hydraulic fracturing. Our anisotropic modeling tool can be used to generate and analyze microseismic full wavefield with full moment tensor source in anisotropic media, which can help promote the anisotropic interpretation and inversion of field data.

Microseismic Full Waveform Modeling in Anisotropic Media with Moment Tensor Implementation

NASA Astrophysics Data System (ADS)

Shi, Peidong; Angus, Doug; Nowacki, Andy; Yuan, Sanyi; Wang, Yanyan

2018-07-01

Seismic anisotropy which is common in shale and fractured rocks will cause travel-time and amplitude discrepancy in different propagation directions. For microseismic monitoring which is often implemented in shale or fractured rocks, seismic anisotropy needs to be carefully accounted for in source location and mechanism determination. We have developed an efficient finite-difference full waveform modeling tool with an arbitrary moment tensor source. The modeling tool is suitable for simulating wave propagation in anisotropic media for microseismic monitoring. As both dislocation and non-double-couple source are often observed in microseismic monitoring, an arbitrary moment tensor source is implemented in our forward modeling tool. The increments of shear stress are equally distributed on the staggered grid to implement an accurate and symmetric moment tensor source. Our modeling tool provides an efficient way to obtain the Green's function in anisotropic media, which is the key of anisotropic moment tensor inversion and source mechanism characterization in microseismic monitoring. In our research, wavefields in anisotropic media have been carefully simulated and analyzed in both surface array and downhole array. The variation characteristics of travel-time and amplitude of direct P- and S-wave in vertical transverse isotropic media and horizontal transverse isotropic media are distinct, thus providing a feasible way to distinguish and identify the anisotropic type of the subsurface. Analyzing the travel-times and amplitudes of the microseismic data is a feasible way to estimate the orientation and density of the induced cracks in hydraulic fracturing. Our anisotropic modeling tool can be used to generate and analyze microseismic full wavefield with full moment tensor source in anisotropic media, which can help promote the anisotropic interpretation and inversion of field data.

Quantum computing on encrypted data

NASA Astrophysics Data System (ADS)

Fisher, K. A. G.; Broadbent, A.; Shalm, L. K.; Yan, Z.; Lavoie, J.; Prevedel, R.; Jennewein, T.; Resch, K. J.

2014-01-01

The ability to perform computations on encrypted data is a powerful tool for protecting privacy. Recently, protocols to achieve this on classical computing systems have been found. Here, we present an efficient solution to the quantum analogue of this problem that enables arbitrary quantum computations to be carried out on encrypted quantum data. We prove that an untrusted server can implement a universal set of quantum gates on encrypted quantum bits (qubits) without learning any information about the inputs, while the client, knowing the decryption key, can easily decrypt the results of the computation. We experimentally demonstrate, using single photons and linear optics, the encryption and decryption scheme on a set of gates sufficient for arbitrary quantum computations. As our protocol requires few extra resources compared with other schemes it can be easily incorporated into the design of future quantum servers. These results will play a key role in enabling the development of secure distributed quantum systems.

Self-replicating machines in continuous space with virtual physics.

PubMed

Smith, Arnold; Turney, Peter; Ewaschuk, Robert

2003-01-01

JohnnyVon is an implementation of self-replicating machines in continuous two-dimensional space. Two types of particles drift about in a virtual liquid. The particles are automata with discrete internal states but continuous external relationships. Their internal states are governed by finite state machines, but their external relationships are governed by a simulated physics that includes Brownian motion, viscosity, and springlike attractive and repulsive forces. The particles can be assembled into patterns that can encode arbitrary strings of bits. We demonstrate that, if an arbitrary seed pattern is put in a soup of separate individual particles, the pattern will replicate by assembling the individual particles into copies of itself. We also show that, given sufficient time, a soup of separate individual particles will eventually spontaneously form self-replicating patterns. We discuss the implications of JohnnyVon for research in nanotechnology, theoretical biology, and artificial life.

Efficient numerical method of freeform lens design for arbitrary irradiance shaping

NASA Astrophysics Data System (ADS)

Wojtanowski, Jacek

2018-05-01

A computational method to design a lens with a flat entrance surface and a freeform exit surface that can transform a collimated, generally non-uniform input beam into a beam with a desired irradiance distribution of arbitrary shape is presented. The methodology is based on non-linear elliptic partial differential equations, known as Monge-Ampère PDEs. This paper describes an original numerical algorithm to solve this problem by applying the Gauss-Seidel method with simplified boundary conditions. A joint MATLAB-ZEMAX environment is used to implement and verify the method. To prove the efficiency of the proposed approach, an exemplary study where the designed lens is faced with the challenging illumination task is shown. An analysis of solution stability, iteration-to-iteration ray mapping evolution (attached in video format), depth of focus and non-zero étendue efficiency is performed.

Multisensor robotic system for autonomous space maintenance and repair

NASA Technical Reports Server (NTRS)

Abidi, M. A.; Green, W. L.; Chandra, T.; Spears, J.

1988-01-01

The feasibility of realistic autonomous space manipulation tasks using multisensory information is demonstrated. The system is capable of acquiring, integrating, and interpreting multisensory data to locate, mate, and demate a Fluid Interchange System (FIS) and a Module Interchange System (MIS). In both cases, autonomous location of a guiding light target, mating, and demating of the system are performed. Implemented visio-driven techniques are used to determine the arbitrary two-dimensional position and orientation of the mating elements as well as the arbitrary three-dimensional position and orientation of the light targets. A force/torque sensor continuously monitors the six components of force and torque exerted on the end-effector. Both FIS and MIS experiments were successfully accomplished on mock-ups built for this purpose. The method is immune to variations in the ambient light, in particular because of the 90-minute day-night shift in space.

Quantum computing on encrypted data.

PubMed

Fisher, K A G; Broadbent, A; Shalm, L K; Yan, Z; Lavoie, J; Prevedel, R; Jennewein, T; Resch, K J

2014-01-01

The ability to perform computations on encrypted data is a powerful tool for protecting privacy. Recently, protocols to achieve this on classical computing systems have been found. Here, we present an efficient solution to the quantum analogue of this problem that enables arbitrary quantum computations to be carried out on encrypted quantum data. We prove that an untrusted server can implement a universal set of quantum gates on encrypted quantum bits (qubits) without learning any information about the inputs, while the client, knowing the decryption key, can easily decrypt the results of the computation. We experimentally demonstrate, using single photons and linear optics, the encryption and decryption scheme on a set of gates sufficient for arbitrary quantum computations. As our protocol requires few extra resources compared with other schemes it can be easily incorporated into the design of future quantum servers. These results will play a key role in enabling the development of secure distributed quantum systems.

Simulating Wake Vortex Detection with the Sensivu Doppler Wind Lidar Simulator

NASA Technical Reports Server (NTRS)

Ramsey, Dan; Nguyen, Chi

2014-01-01

In support of NASA's Atmospheric Environment Safety Technologies NRA research topic on Wake Vortex Hazard Investigation, Aerospace Innovations (AI) investigated a set of techniques for detecting wake vortex hazards from arbitrary viewing angles, including axial perspectives. This technical report describes an approach to this problem and presents results from its implementation in a virtual lidar simulator developed at AI. Threedimensional data volumes from NASA's Terminal Area Simulation System (TASS) containing strong turbulent vortices were used as the atmospheric domain for these studies, in addition to an analytical vortex model in 3-D space. By incorporating a third-party radiative transfer code (BACKSCAT 4), user-defined aerosol layers can be incorporated into atmospheric models, simulating attenuation and backscatter in different environmental conditions and altitudes. A hazard detection algorithm is described that uses a twocomponent spectral model to identify vortex signatures observable from arbitrary angles.

Automatic generation of efficient array redistribution routines for distributed memory multicomputers

NASA Technical Reports Server (NTRS)

Ramaswamy, Shankar; Banerjee, Prithviraj

1994-01-01

Appropriate data distribution has been found to be critical for obtaining good performance on Distributed Memory Multicomputers like the CM-5, Intel Paragon and IBM SP-1. It has also been found that some programs need to change their distributions during execution for better performance (redistribution). This work focuses on automatically generating efficient routines for redistribution. We present a new mathematical representation for regular distributions called PITFALLS and then discuss algorithms for redistribution based on this representation. One of the significant contributions of this work is being able to handle arbitrary source and target processor sets while performing redistribution. Another important contribution is the ability to handle an arbitrary number of dimensions for the array involved in the redistribution in a scalable manner. Our implementation of these techniques is based on an MPI-like communication library. The results presented show the low overheads for our redistribution algorithm as compared to naive runtime methods.

Cafe: A Generic Configurable Customizable Composite Cloud Application Framework

NASA Astrophysics Data System (ADS)

Mietzner, Ralph; Unger, Tobias; Leymann, Frank

In this paper we present Cafe (Composite Application Framework) an approach to describe configurable composite service-oriented applications and to automatically provision them across different providers. Cafe enables independent software vendors to describe their composite service-oriented applications and the components that are used to assemble them. Components can be internal to the application or external and can be deployed in any of the delivery models present in the cloud. The components are annotated with requirements for the infrastructure they later need to be run on. Providers on the other hand advertise their infrastructure services by describing them as infrastructure capabilities. The separation of software vendors and providers enables end users and providers to follow a best-of-breed strategy by combining arbitrary applications with arbitrary providers. We show how such applications can be automatically provisioned and present an architecture and a prototype that implements the concepts.

Quantum State Transmission in a Superconducting Charge Qubit-Atom Hybrid

PubMed Central

Yu, Deshui; Valado, María Martínez; Hufnagel, Christoph; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2016-01-01

Hybrids consisting of macroscopic superconducting circuits and microscopic components, such as atoms and spins, have the potential of transmitting an arbitrary state between different quantum species, leading to the prospective of high-speed operation and long-time storage of quantum information. Here we propose a novel hybrid structure, where a neutral-atom qubit directly interfaces with a superconducting charge qubit, to implement the qubit-state transmission. The highly-excited Rydberg atom located inside the gate capacitor strongly affects the behavior of Cooper pairs in the box while the atom in the ground state hardly interferes with the superconducting device. In addition, the DC Stark shift of the atomic states significantly depends on the charge-qubit states. By means of the standard spectroscopic techniques and sweeping the gate voltage bias, we show how to transfer an arbitrary quantum state from the superconducting device to the atom and vice versa. PMID:27922087

Versatile fusion source integrator AFSI for fast ion and neutron studies in fusion devices

NASA Astrophysics Data System (ADS)

Sirén, Paula; Varje, Jari; Äkäslompolo, Simppa; Asunta, Otto; Giroud, Carine; Kurki-Suonio, Taina; Weisen, Henri; JET Contributors, The

2018-01-01

ASCOT Fusion Source Integrator AFSI, an efficient tool for calculating fusion reaction rates and characterizing the fusion products, based on arbitrary reactant distributions, has been developed and is reported in this paper. Calculation of reactor-relevant D-D, D-T and D-3He fusion reactions has been implemented based on the Bosch-Hale fusion cross sections. The reactions can be calculated between arbitrary particle populations, including Maxwellian thermal particles and minority energetic particles. Reaction rate profiles, energy spectra and full 4D phase space distributions can be calculated for the non-isotropic reaction products. The code is especially suitable for integrated modelling in self-consistent plasma physics simulations as well as in the Serpent neutronics calculation chain. Validation of the model has been performed for neutron measurements at the JET tokamak and the code has been applied to predictive simulations in ITER.

Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

EPA Science Inventory

With increasing knowledge about the potential mechanisms underlying cellular functions, it is becoming feasible to predict the response of biological systems to genetic and environmental perturbations. Due to the lack of homogeneity in living tissues it is difficult to estimate t...

A Boolean Network Model of Nuclear Receptor Mediated Cell Cycle Progression

EPA Science Inventory

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate a broad range of cellular processes. Hormones, lipids and xenobiotics have been shown to activate NRs with a range of consequences on development, metabolism, oxidative stress, apoptosis, and prolif...

A Boolean Network Model of Nuclear Receptor Mediated Cell Cycle Progression (S)

EPA Science Inventory

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate a broad range of cellular processes. Hormones, lipids and xenobiotics have been shown to activate NRs with a range of consequences on development, metabolism, oxidative stress, apoptosis, and prolif...

Automatic Query Formulations in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1983-01-01

Introduces methods designed to reduce role of search intermediaries by generating Boolean search formulations automatically using term frequency considerations from natural language statements provided by system patrons. Experimental results are supplied and methods are described for applying automatic query formulation process in practice.…

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Topics for Mathematics Clubs.

ERIC Educational Resources Information Center

Dalton, LeRoy C., Ed.; Snyder, Henry D., Ed.

The ten chapters in this booklet cover topics not ordinarily discussed in the classroom: Fibonacci sequences, projective geometry, groups, infinity and transfinite numbers, Pascal's Triangle, topology, experiments with natural numbers, non-Euclidean geometries, Boolean algebras, and the imaginary and the infinite in geometry. Each chapter is…

Coherent optical pulse sequencer for quantum applications.

PubMed

Hosseini, Mahdi; Sparkes, Ben M; Hétet, Gabriel; Longdell, Jevon J; Lam, Ping Koy; Buchler, Ben C

2009-09-10

The bandwidth and versatility of optical devices have revolutionized information technology systems and communication networks. Precise and arbitrary control of an optical field that preserves optical coherence is an important requisite for many proposed photonic technologies. For quantum information applications, a device that allows storage and on-demand retrieval of arbitrary quantum states of light would form an ideal quantum optical memory. Recently, significant progress has been made in implementing atomic quantum memories using electromagnetically induced transparency, photon echo spectroscopy, off-resonance Raman spectroscopy and other atom-light interaction processes. Single-photon and bright-optical-field storage with quantum states have both been successfully demonstrated. Here we present a coherent optical memory based on photon echoes induced through controlled reversible inhomogeneous broadening. Our scheme allows storage of multiple pulses of light within a chosen frequency bandwidth, and stored pulses can be recalled in arbitrary order with any chosen delay between each recalled pulse. Furthermore, pulses can be time-compressed, time-stretched or split into multiple smaller pulses and recalled in several pieces at chosen times. Although our experimental results are so far limited to classical light pulses, our technique should enable the construction of an optical random-access memory for time-bin quantum information, and have potential applications in quantum information processing.

Hardware for dynamic quantum computing experiments: Part I

NASA Astrophysics Data System (ADS)

Johnson, Blake; Ryan, Colm; Riste, Diego; Donovan, Brian; Ohki, Thomas

Static, pre-defined control sequences routinely achieve high-fidelity operation on superconducting quantum processors. Efforts toward dynamic experiments depending on real-time information have mostly proceeded through hardware duplication and triggers, requiring a combinatorial explosion in the number of channels. We provide a hardware efficient solution to dynamic control with a complete platform of specialized FPGA-based control and readout electronics; these components enable arbitrary control flow, low-latency feedback and/or feedforward, and scale far beyond single-qubit control and measurement. We will introduce the BBN Arbitrary Pulse Sequencer 2 (APS2) control system and the X6 QDSP readout platform. The BBN APS2 features: a sequencer built around implementing short quantum gates, a sequence cache to allow long sequences with branching structures, subroutines for code re-use, and a trigger distribution module to capture and distribute steering information. The X6 QDSP features a single-stage DSP pipeline that combines demodulation with arbitrary integration kernels, and multiple taps to inspect data flow for debugging and calibration. We will show system performance when putting it all together, including a latency budget for feedforward operations. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Contract No. W911NF-10-1-0324.

Adaptiveness in monotone pseudo-Boolean optimization and stochastic neural computation.

PubMed

Grossi, Giuliano

2009-08-01

Hopfield neural network (HNN) is a nonlinear computational model successfully applied in finding near-optimal solutions of several difficult combinatorial problems. In many cases, the network energy function is obtained through a learning procedure so that its minima are states falling into a proper subspace (feasible region) of the search space. However, because of the network nonlinearity, a number of undesirable local energy minima emerge from the learning procedure, significantly effecting the network performance. In the neural model analyzed here, we combine both a penalty and a stochastic process in order to enhance the performance of a binary HNN. The penalty strategy allows us to gradually lead the search towards states representing feasible solutions, so avoiding oscillatory behaviors or asymptotically instable convergence. Presence of stochastic dynamics potentially prevents the network to fall into shallow local minima of the energy function, i.e., quite far from global optimum. Hence, for a given fixed network topology, the desired final distribution on the states can be reached by carefully modulating such process. The model uses pseudo-Boolean functions both to express problem constraints and cost function; a combination of these two functions is then interpreted as energy of the neural network. A wide variety of NP-hard problems fall in the class of problems that can be solved by the model at hand, particularly those having a monotonic quadratic pseudo-Boolean function as constraint function. That is, functions easily derived by closed algebraic expressions representing the constraint structure and easy (polynomial time) to maximize. We show the asymptotic convergence properties of this model characterizing its state space distribution at thermal equilibrium in terms of Markov chain and give evidence of its ability to find high quality solutions on benchmarks and randomly generated instances of two specific problems taken from the computational graph theory.

Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming.

PubMed

Chebouba, Lokmane; Miannay, Bertrand; Boughaci, Dalila; Guziolowski, Carito

2018-03-08

During the last years, several approaches were applied on biomedical data to detect disease specific proteins and genes in order to better target drugs. It was shown that statistical and machine learning based methods use mainly clinical data and improve later their results by adding omics data. This work proposes a new method to discriminate the response of Acute Myeloid Leukemia (AML) patients to treatment. The proposed approach uses proteomics data and prior regulatory knowledge in the form of networks to predict cancer treatment outcomes by finding out the different Boolean networks specific to each type of response to drugs. To show its effectiveness we evaluate our method on a dataset from the DREAM 9 challenge. The results are encouraging and demonstrate the benefit of our approach to distinguish patient groups with different response to treatment. In particular each treatment response group is characterized by a predictive model in the form of a signaling Boolean network. This model describes regulatory mechanisms which are specific to each response group. The proteins in this model were selected from the complete dataset by imposing optimization constraints that maximize the difference in the logical response of the Boolean network associated to each group of patients given the omic dataset. This mechanistic and predictive model also allow us to classify new patients data into the two different patient response groups. We propose a new method to detect the most relevant proteins for understanding different patient responses upon treatments in order to better target drugs using a Prior Knowledge Network and proteomics data. The results are interesting and show the effectiveness of our method.

Intelligent Machines in the 21st Century: Automating the Processes of Inference and Inquiry

NASA Technical Reports Server (NTRS)

Knuth, Kevin H.

2003-01-01

The last century saw the application of Boolean algebra toward the construction of computing machines, which work by applying logical transformations to information contained in their memory. The development of information theory and the generalization of Boolean algebra to Bayesian inference have enabled these computing machines. in the last quarter of the twentieth century, to be endowed with the ability to learn by making inferences from data. This revolution is just beginning as new computational techniques continue to make difficult problems more accessible. However, modern intelligent machines work by inferring knowledge using only their pre-programmed prior knowledge and the data provided. They lack the ability to ask questions, or request data that would aid their inferences. Recent advances in understanding the foundations of probability theory have revealed implications for areas other than logic. Of relevance to intelligent machines, we identified the algebra of questions as the free distributive algebra, which now allows us to work with questions in a way analogous to that which Boolean algebra enables us to work with logical statements. In this paper we describe this logic of inference and inquiry using the mathematics of partially ordered sets and the scaffolding of lattice theory, discuss the far-reaching implications of the methodology, and demonstrate its application with current examples in machine learning. Automation of both inference and inquiry promises to allow robots to perform science in the far reaches of our solar system and in other star systems by enabling them to not only make inferences from data, but also decide which question to ask, experiment to perform, or measurement to take given what they have learned and what they are designed to understand.

Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model

PubMed Central

Lu, Wei; Song, Jiangning; Akutsu, Tatsuya

2015-01-01

Abstract This article considers the problem whereby, given two metabolic networks N1 and N2, a set of source compounds, and a set of target compounds, we must find the minimum set of reactions whose removal (knockout) ensures that the target compounds are not producible in N1 but are producible in N2. Similar studies exist for the problem of finding the minimum knockout with the smallest side effect for a single network. However, if technologies of external perturbations are advanced in the near future, it may be important to develop methods of computing the minimum knockout for multiple networks (MKMN). Flux balance analysis (FBA) is efficient if a well-polished model is available. However, that is not always the case. Therefore, in this article, we study MKMN in Boolean models and an elementary mode (EM)-based model. Integer linear programming (ILP)-based methods are developed for these models, since MKMN is NP-complete for both the Boolean model and the EM-based model. Computer experiments are conducted with metabolic networks of clostridium perfringens SM101 and bifidobacterium longum DJO10A, respectively known as bad bacteria and good bacteria for the human intestine. The results show that larger networks are more likely to have MKMN solutions. However, solving for these larger networks takes a very long time, and often the computation cannot be completed. This is reasonable, because small networks do not have many alternative pathways, making it difficult to satisfy the MKMN condition, whereas in large networks the number of candidate solutions explodes. Our developed software minFvskO is available online. PMID:25684199

Transient Finite Element Computations on a Variable Transputer System

NASA Technical Reports Server (NTRS)

Smolinski, Patrick J.; Lapczyk, Ireneusz

1993-01-01

A parallel program to analyze transient finite element problems was written and implemented on a system of transputer processors. The program uses the explicit time integration algorithm which eliminates the need for equation solving, making it more suitable for parallel computations. An interprocessor communication scheme was developed for arbitrary two dimensional grid processor configurations. Several 3-D problems were analyzed on a system with a small number of processors.

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

Moryakov, A. V., E-mail: sailor@yauza.ru; Pylyov, S. S.

This paper presents the formulation of the problem and the methodical approach for solving large systems of linear differential equations describing nonstationary processes with the use of CUDA technology; this approach is implemented in the ANGEL program. Results for a test problem on transport of radioactive products over loops of a nuclear power plant are given. The possibilities for the use of the ANGEL program for solving various problems that simulate arbitrary nonstationary processes are discussed.

Applying Image Matching to Video Analysis

DTIC Science & Technology

2010-09-01

image groups, classified by the background scene, are the flag, the kitchen, the telephone, the bookshelf , the title screen, the...Kitchen 136 Telephone 3 Bookshelf 81 Title Screen 10 Map 1 24 Map 2 16 command line. This implementation of a Bloom filter uses two arbitrary...with the Bookshelf images. This scene is a much closer shot than the Kitchen scene so the host occupies much of the background. Algorithms for face

Extended computational kernels in a massively parallel implementation of the Trotter-Suzuki approximation

NASA Astrophysics Data System (ADS)

Wittek, Peter; Calderaro, Luca

2015-12-01

We extended a parallel and distributed implementation of the Trotter-Suzuki algorithm for simulating quantum systems to study a wider range of physical problems and to make the library easier to use. The new release allows periodic boundary conditions, many-body simulations of non-interacting particles, arbitrary stationary potential functions, and imaginary time evolution to approximate the ground state energy. The new release is more resilient to the computational environment: a wider range of compiler chains and more platforms are supported. To ease development, we provide a more extensive command-line interface, an application programming interface, and wrappers from high-level languages.

Sequence invariant state machines

NASA Technical Reports Server (NTRS)

Whitaker, S.; Manjunath, S.

1990-01-01

A synthesis method and new VLSI architecture are introduced to realize sequential circuits that have the ability to implement any state machine having N states and m inputs, regardless of the actual sequence specified in the flow table. A design method is proposed that utilizes BTS logic to implement regular and dense circuits. A given state sequence can be programmed with power supply connections or dynamically reallocated if stored in a register. Arbitrary flow table sequences can be modified or programmed to dynamically alter the function of the machine. This allows VLSI controllers to be designed with the programmability of a general purpose processor but with the compact size and performance of dedicated logic.

Make Mine a Metasearcher, Please!

ERIC Educational Resources Information Center

Repman, Judi; Carlson, Randal D.

2000-01-01

Describes metasearch tools and explains their value in helping library media centers improve students' Web searches. Discusses Boolean queries and the emphasis on speed at the expense of comprehensiveness; and compares four metasearch tools, including the number of search engines consulted, user control, and databases included. (LRW)

Boolean Approaches in Digital Diagnosis

DTIC Science & Technology

1989-12-04

Automation Conference, pages 64-70, 1983. 16. Barry W. Johnson. Design and A nalysis of Fault-Tolerant Digital Systems. Addison- Wesley Publishing...Mitchell. On a new algebra of logic. In C.S. Peirce, edhitor, Studies in Logic. Little, Brown. Boston. 1883. 2:3. Roger S. Pressman . Softwrare Engineering

Presentation of Repeated Phrases in a Computer-Assisted Abstracting Tool Kit.

ERIC Educational Resources Information Center

Craven, Timothy C.

2001-01-01

Discusses automatic indexing methods and describes the development of a prototype computerized abstractor's assistant. Highlights include the text network management system, TEXNET; phrase selection that follows indexing; phrase display, including Boolean capabilities; results of preliminary testing; and availability of TEXNET software. (LRW)

Stochastic Pseudo-Boolean Optimization

DTIC Science & Technology

2011-07-31

Right-Hand Side,” 2009 IN- FORMS Annual Meeting, San Diego, CA, October 11-14, 2009. 113 References [1] A.-Ghouila-Houri. Caracterisation des matrices...Optimization, 10:7–21, 2005. [30] P. Camion. Caracterisation des matrices unimodulaires. Cahiers Centre Etudes Rech., 5(4), 1963. [31] P. Camion

Order or chaos in Boolean gene networks depends on the mean fraction of canalizing functions

NASA Astrophysics Data System (ADS)

Karlsson, Fredrik; Hörnquist, Michael

2007-10-01

We explore the connection between order/chaos in Boolean networks and the naturally occurring fraction of canalizing functions in such systems. This fraction turns out to give a very clear indication of whether the system possesses ordered or chaotic dynamics, as measured by Derrida plots, and also the degree of order when we compare different networks with the same number of vertices and edges. By studying also a wide distribution of indegrees in a network, we show that the mean probability of canalizing functions is a more reliable indicator of the type of dynamics for a finite network than the classical result on stability relating the bias to the mean indegree. Finally, we compare by direct simulations two biologically derived networks with networks of similar sizes but with power-law and Poisson distributions of indegrees, respectively. The biologically motivated networks are not more ordered than the latter, and in one case the biological network is even chaotic while the others are not.

Two classes of ODE models with switch-like behavior.

PubMed

Just, Winfried; Korb, Mason; Elbert, Ben; Young, Todd

2013-12-01

In cases where the same real-world system can be modeled both by an ODE system ⅅ and a Boolean system , it is of interest to identify conditions under which the two systems will be consistent, that is, will make qualitatively equivalent predictions. In this note we introduce two broad classes of relatively simple models that provide a convenient framework for studying such questions. In contrast to the widely known class of Glass networks, the right-hand sides of our ODEs are Lipschitz-continuous. We prove that if has certain structures, consistency between ⅅ and is implied by sufficient separation of time scales in one class of our models. Namely, if the trajectories of are "one-stepping" then we prove a strong form of consistency and if has a certain monotonicity property then there is a weaker consistency between ⅅ and . These results appear to point to more general structure properties that favor consistency between ODE and Boolean models.

Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space

NASA Astrophysics Data System (ADS)

Szejka, Agnes; Drossel, Barbara

2010-02-01

We study the evolution of Boolean networks as model systems for gene regulation. Inspired by biological networks, we select simultaneously for robust attractors and for the ability to respond to external inputs by changing the attractor. Mutations change the connections between the nodes and the update functions. In order to investigate the influence of the type of update functions, we perform our simulations with canalizing as well as with threshold functions. We compare the properties of the fitness landscapes that result for different versions of the selection criterion and the update functions. We find that for all studied cases the fitness landscape has a plateau with maximum fitness resulting in the fact that structurally very different networks are able to fulfill the same task and are connected by neutral paths in network (“genotype”) space. We find furthermore a connection between the attractor length and the mutational robustness, and an extremely long memory of the initial evolutionary stage.

Comparison of Seven Methods for Boolean Factor Analysis and Their Evaluation by Information Gain.

PubMed

Frolov, Alexander A; Húsek, Dušan; Polyakov, Pavel Yu

2016-03-01

An usual task in large data set analysis is searching for an appropriate data representation in a space of fewer dimensions. One of the most efficient methods to solve this task is factor analysis. In this paper, we compare seven methods for Boolean factor analysis (BFA) in solving the so-called bars problem (BP), which is a BFA benchmark. The performance of the methods is evaluated by means of information gain. Study of the results obtained in solving BP of different levels of complexity has allowed us to reveal strengths and weaknesses of these methods. It is shown that the Likelihood maximization Attractor Neural Network with Increasing Activity (LANNIA) is the most efficient BFA method in solving BP in many cases. Efficacy of the LANNIA method is also shown, when applied to the real data from the Kyoto Encyclopedia of Genes and Genomes database, which contains full genome sequencing for 1368 organisms, and to text data set R52 (from Reuters 21578) typically used for label categorization.

Intrication temporelle et communication quantique

NASA Astrophysics Data System (ADS)

Bussieres, Felix

Quantum communication is the art of transferring a quantum state from one place to another and the study of tasks that can be accomplished with it. This thesis is devoted to the development of tools and tasks for quantum communication in a real-world setting. These were implemented using an underground optical fibre link deployed in an urban environment. The technological and theoretical innovations presented here broaden the range of applications of time-bin entanglement through new methods of manipulating time-bin qubits, a novel model for characterizing sources of photon pairs, new ways of testing non-locality and the design and the first implementation of a new loss-tolerant quantum coin-flipping protocol. Manipulating time-bin qubits. A single photon is an excellent vehicle in which a qubit, the fundamental unit of quantum information, can be encoded. In particular, the time-bin encoding of photonic qubits is well suited for optical fibre transmission. Before this thesis, the applications of quantum communication based on the time-bin encoding were limited due to the lack of methods to implement arbitrary operations and measurements. We have removed this restriction by proposing the first methods to realize arbitrary deterministic operations on time-bin qubits as well as single qubit measurements in an arbitrary basis. We applied these propositions to the specific case of optical measurement-based quantum computing and showed how to implement the feedforward operations, which are essential to this model. This therefore opens new possibilities for creating an optical quantum computer, but also for other quantum communication tasks. Characterizing sources of photon pairs. Experimental quantum communication requires the creation of single photons and entangled photons. These two ingredients can be obtained from a source of photon pairs based on non-linear spontaneous processes. Several tasks in quantum communication require a precise knowledge of the properties of the source being used. We developed and implemented a fast and simple method to characterize a source of photon pairs. This method is well suited for a realistic setting where experimental conditions, such as channel transmittance, may fluctuate, and for which the characterization of the source has to be done in real time. Testing the non-locality of time-bin entanglement. Entanglement is a resource needed for the realization of many important tasks in quantum communication. It also allows two physical systems to be correlated in a way that cannot be explained by classical physics; this manifestation of entanglement is called non-locality. We built a source of time-bin entangled photonic qubits and characterized it with the new methods implementing arbitrary single qubit measurements that we developed. This allowed us to reveal the non-local nature of our source of entanglement in ways that were never implemented before. It also opens the door to study previously untested features of non-locality using this source. Theses experiments were performed in a realistic setting where quantum (non-local) correlations were observed even after transmission of one of the entangled qubits over 12.4 km of an underground optical fibre. Flipping quantum coins. Quantum coin-flipping is a quantum cryptographic primitive proposed in 1984, that is when the very first steps of quantum communication were being taken, where two players alternate in sending classical and quantum information in order to generate a shared random bit. The use of quantum information is such that a potential cheater cannot force the outcome to his choice with certainty. Classically, however, one of the players can always deterministically choose the outcome. Unfortunately, the security of all previous quantum coin-flipping protocols is seriously compromised in the presence of losses on the transmission channel, thereby making this task impractical. We found a solution to this problem and obtained the first loss-tolerant quantum coin-flipping protocol whose security is independent of the amount of the losses. We have also experimentally demonstrated our loss-tolerant protocol using our source of time-bin entanglement combined with our arbitrary single qubit measurement methods. This experiment took place in a realistic setting where qubits travelled over an underground optical fibre link. This new task thus joins quantum key distribution as a practical application of quantum communication. Keywords. quantum communication, photonics, time-bin encoding, source of photon pairs, heralded single photon source, entanglement, non-locality, time-bin entanglement, hybrid entanglement, quantum network, quantum cryptography, quantum coin-flipping, measurement-based quantum computation, telecommunication, optical fibre, nonlinear optics.

Adiabatic quantum games and phase-transition-like behavior between optimal strategies

NASA Astrophysics Data System (ADS)

de Ponte, M. A.; Santos, Alan C.

2018-06-01

In this paper we propose a game of a single qubit whose strategies can be implemented adiabatically. In addition, we show how to implement the strategies of a quantum game through controlled adiabatic evolutions, where we analyze the payment of a quantum player for various situations of interest: (1) when the players receive distinct payments, (2) when the initial state is an arbitrary superposition, and (3) when the device that implements the strategy is inefficient. Through a graphical analysis, it is possible to notice that the curves that represent the gains of the players present a behavior similar to the curves that give rise to a phase transition in thermodynamics. These transitions are associated with optimal strategy changes and occur in the absence of entanglement and interaction between the players.

Weak form implementation of the semi-analytical finite element (SAFE) method for a variety of elastodynamic waveguides

NASA Astrophysics Data System (ADS)

Hakoda, Christopher; Lissenden, Clifford; Rose, Joseph L.

2018-04-01

Dispersion curves are essential to any guided wave NDE project. The Semi-Analytical Finite Element (SAFE) method has significantly increased the ease by which these curves can be calculated. However, due to misconceptions regarding theory and fragmentation based on different finite-element software, the theory has stagnated, and adoption by researchers who are new to the field has been slow. This paper focuses on the relationship between the SAFE formulation and finite element theory, and the implementation of the SAFE method in a weak form for plates, pipes, layered waveguides/composites, curved waveguides, and arbitrary cross-sections is shown. The benefits of the weak form are briefly described, as is implementation in open-source and commercial finite element software.

Computationally efficient method for optical simulation of solar cells and their applications

NASA Astrophysics Data System (ADS)

Semenikhin, I.; Zanuccoli, M.; Fiegna, C.; Vyurkov, V.; Sangiorgi, E.

2013-01-01

This paper presents two novel implementations of the Differential method to solve the Maxwell equations in nanostructured optoelectronic solid state devices. The first proposed implementation is based on an improved and computationally efficient T-matrix formulation that adopts multiple-precision arithmetic to tackle the numerical instability problem which arises due to evanescent modes. The second implementation adopts the iterative approach that allows to achieve low computational complexity O(N logN) or better. The proposed algorithms may work with structures with arbitrary spatial variation of the permittivity. The developed two-dimensional numerical simulator is applied to analyze the dependence of the absorption characteristics of a thin silicon slab on the morphology of the front interface and on the angle of incidence of the radiation with respect to the device surface.

A fast template periodogram

NASA Astrophysics Data System (ADS)

Hoffman, John; VanderPlas, Jake; Hartman, Joel; Bakos, Gáspár

2017-09-01

This proceedings contribution presents a novel, non-linear extension to the Lomb-Scargle periodogram that allows periodograms to be generated for arbitrary signal shapes. Such periodograms are already known as "template periodograms" or "periodic matched filters," but current implementations are computationally inefficient. The "fast template periodogram" presented here improves existing techniques by a factor of ˜a few for small test cases (O(10) observations), and over three orders of magnitude for lightcurves containing O(104) observations. The fast template periodogram scales asymptotically as O(HNf log HNf + H4Nf), where H denotes the number of harmonics required to adequately approximate the template and Nf is the number of trial frequencies. Existing implementations scale as O(NobsNf), where Nobs is the number of observations in the lightcurve. An open source Python implementation is available on GitHub.

Novel strategy to implement active-space coupled-cluster methods

NASA Astrophysics Data System (ADS)

Rolik, Zoltán; Kállay, Mihály

2018-03-01

A new approach is presented for the efficient implementation of coupled-cluster (CC) methods including higher excitations based on a molecular orbital space partitioned into active and inactive orbitals. In the new framework, the string representation of amplitudes and intermediates is used as long as it is beneficial, but the contractions are evaluated as matrix products. Using a new diagrammatic technique, the CC equations are represented in a compact form due to the string notations we introduced. As an application of these ideas, a new automated implementation of the single-reference-based multi-reference CC equations is presented for arbitrary excitation levels. The new program can be considered as an improvement over the previous implementations in many respects; e.g., diagram contributions are evaluated by efficient vectorized subroutines. Timings for test calculations for various complete active-space problems are presented. As an application of the new code, the weak interactions in the Be dimer were studied.

Efficient implementation of arbitrary quantum state engineering in four-state system by counterdiabatic driving

NASA Astrophysics Data System (ADS)

Wang, Song-Bai; Chen, Ye-Hong; Wu, Qi-Cheng; Shi, Zhi-Cheng; Huang, Bi-Hua; Song, Jie; Xia, Yan

2018-07-01

A scheme is proposed to implement quantum state engineering (QSE) in a four-state system via counterdiabatic driving. In the scheme, single- and multi-mode driving methods are used respectively to drive the system to a target state at a predefined time. It is found that a fast QSE can be realized by utilizing simply designed pulses. In addition, a beneficial discussion on the energy consumption between the single- and multi-mode driving protocols shows that the multi-mode driving method seems to have a wider range of applications than the single-mode driving method with respect to different parameters. Finally, the scheme is also helpful for implementing the generalization QSE in high-dimensional systems via the concept of a dressed state. Therefore, the scheme can be implemented with the present experimental technology, which is useful in quantum information processing.