Computer modeling of properties of complex molecular systems

Energy Technology Data Exchange (ETDEWEB)

Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

2015-03-10

Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.

Infinite possibilities: Computational structures technology

Science.gov (United States)

Beam, Sherilee F.

1994-12-01

Computational Fluid Dynamics (or CFD) methods are very familiar to the research community. Even the general public has had some exposure to CFD images, primarily through the news media. However, very little attention has been paid to CST--Computational Structures Technology. Yet, no important design can be completed without it. During the first half of this century, researchers only dreamed of designing and building structures on a computer. Today their dreams have become practical realities as computational methods are used in all phases of design, fabrication and testing of engineering systems. Increasingly complex structures can now be built in even shorter periods of time. Over the past four decades, computer technology has been developing, and early finite element methods have grown from small in-house programs to numerous commercial software programs. When coupled with advanced computing systems, they help engineers make dramatic leaps in designing and testing concepts. The goals of CST include: predicting how a structure will behave under actual operating conditions; designing and complementing other experiments conducted on a structure; investigating microstructural damage or chaotic, unpredictable behavior; helping material developers in improving material systems; and being a useful tool in design systems optimization and sensitivity techniques. Applying CST to a structure problem requires five steps: (1) observe the specific problem; (2) develop a computational model for numerical simulation; (3) develop and assemble software and hardware for running the codes; (4) post-process and interpret the results; and (5) use the model to analyze and design the actual structure. Researchers in both industry and academia continue to make significant contributions to advance this technology with improvements in software, collaborative computing environments and supercomputing systems. As these environments and systems evolve, computational structures technology will

Computational complexity in entanglement transformations

Science.gov (United States)

Chitambar, Eric A.

In physics, systems having three parts are typically much more difficult to analyze than those having just two. Even in classical mechanics, predicting the motion of three interacting celestial bodies remains an insurmountable challenge while the analogous two-body problem has an elementary solution. It is as if just by adding a third party, a fundamental change occurs in the structure of the problem that renders it unsolvable. In this thesis, we demonstrate how such an effect is likewise present in the theory of quantum entanglement. In fact, the complexity differences between two-party and three-party entanglement become quite conspicuous when comparing the difficulty in deciding what state changes are possible for these systems when no additional entanglement is consumed in the transformation process. We examine this entanglement transformation question and its variants in the language of computational complexity theory, a powerful subject that formalizes the concept of problem difficulty. Since deciding feasibility of a specified bipartite transformation is relatively easy, this task belongs to the complexity class P. On the other hand, for tripartite systems, we find the problem to be NP-Hard, meaning that its solution is at least as hard as the solution to some of the most difficult problems humans have encountered. One can then rigorously defend the assertion that a fundamental complexity difference exists between bipartite and tripartite entanglement since unlike the former, the full range of forms realizable by the latter is incalculable (assuming P≠NP). However, similar to the three-body celestial problem, when one examines a special subclass of the problem---invertible transformations on systems having at least one qubit subsystem---we prove that the problem can be solved efficiently. As a hybrid of the two questions, we find that the question of tripartite to bipartite transformations can be solved by an efficient randomized algorithm. Our results are

Cloud Computing for Complex Performance Codes.

Energy Technology Data Exchange (ETDEWEB)

Appel, Gordon John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hadgu, Teklu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Klein, Brandon Thorin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Miner, John Gifford [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-02-01

This report describes the use of cloud computing services for running complex public domain performance assessment problems. The work consisted of two phases: Phase 1 was to demonstrate complex codes, on several differently configured servers, could run and compute trivial small scale problems in a commercial cloud infrastructure. Phase 2 focused on proving non-trivial large scale problems could be computed in the commercial cloud environment. The cloud computing effort was successfully applied using codes of interest to the geohydrology and nuclear waste disposal modeling community.

Nature, computation and complexity

International Nuclear Information System (INIS)

Binder, P-M; Ellis, G F R

2016-01-01

The issue of whether the unfolding of events in the world can be considered a computation is explored in this paper. We come to different conclusions for inert and for living systems (‘no’ and ‘qualified yes’, respectively). We suggest that physical computation as we know it exists only as a tool of complex biological systems: us. (paper)

Hybrid logic on linear structures: expressivity and complexity

NARCIS (Netherlands)

Franceschet, M.; de Rijke, M.; Schlingoff, B.-H.

2003-01-01

We investigate expressivity and complexity of hybrid logics on linear structures. Hybrid logics are an enrichment of modal logics with certain first-order features which are algorithmically well behaved. Therefore, they are well suited for the specification of certain properties of computational

Atomic switch networks—nanoarchitectonic design of a complex system for natural computing

International Nuclear Information System (INIS)

Demis, E C; Aguilera, R; Sillin, H O; Scharnhorst, K; Sandouk, E J; Gimzewski, J K; Aono, M; Stieg, A Z

2015-01-01

Self-organized complex systems are ubiquitous in nature, and the structural complexity of these natural systems can be used as a model to design new classes of functional nanotechnology based on highly interconnected networks of interacting units. Conventional fabrication methods for electronic computing devices are subject to known scaling limits, confining the diversity of possible architectures. This work explores methods of fabricating a self-organized complex device known as an atomic switch network and discusses its potential utility in computing. Through a merger of top-down and bottom-up techniques guided by mathematical and nanoarchitectonic design principles, we have produced functional devices comprising nanoscale elements whose intrinsic nonlinear dynamics and memorization capabilities produce robust patterns of distributed activity and a capacity for nonlinear transformation of input signals when configured in the appropriate network architecture. Their operational characteristics represent a unique potential for hardware implementation of natural computation, specifically in the area of reservoir computing—a burgeoning field that investigates the computational aptitude of complex biologically inspired systems. (paper)

Solving complex band structure problems with the FEAST eigenvalue algorithm

Science.gov (United States)

Laux, S. E.

2012-08-01

With straightforward extension, the FEAST eigenvalue algorithm [Polizzi, Phys. Rev. B 79, 115112 (2009)] is capable of solving the generalized eigenvalue problems representing traveling-wave problems—as exemplified by the complex band-structure problem—even though the matrices involved are complex, non-Hermitian, and singular, and hence outside the originally stated range of applicability of the algorithm. The obtained eigenvalues/eigenvectors, however, contain spurious solutions which must be detected and removed. The efficiency and parallel structure of the original algorithm are unaltered. The complex band structures of Si layers of varying thicknesses and InAs nanowires of varying radii are computed as test problems.

Fluid/Structure Interaction Studies of Aircraft Using High Fidelity Equations on Parallel Computers

Science.gov (United States)

Guruswamy, Guru; VanDalsem, William (Technical Monitor)

1994-01-01

Abstract Aeroelasticity which involves strong coupling of fluids, structures and controls is an important element in designing an aircraft. Computational aeroelasticity using low fidelity methods such as the linear aerodynamic flow equations coupled with the modal structural equations are well advanced. Though these low fidelity approaches are computationally less intensive, they are not adequate for the analysis of modern aircraft such as High Speed Civil Transport (HSCT) and Advanced Subsonic Transport (AST) which can experience complex flow/structure interactions. HSCT can experience vortex induced aeroelastic oscillations whereas AST can experience transonic buffet associated structural oscillations. Both aircraft may experience a dip in the flutter speed at the transonic regime. For accurate aeroelastic computations at these complex fluid/structure interaction situations, high fidelity equations such as the Navier-Stokes for fluids and the finite-elements for structures are needed. Computations using these high fidelity equations require large computational resources both in memory and speed. Current conventional super computers have reached their limitations both in memory and speed. As a result, parallel computers have evolved to overcome the limitations of conventional computers. This paper will address the transition that is taking place in computational aeroelasticity from conventional computers to parallel computers. The paper will address special techniques needed to take advantage of the architecture of new parallel computers. Results will be illustrated from computations made on iPSC/860 and IBM SP2 computer by using ENSAERO code that directly couples the Euler/Navier-Stokes flow equations with high resolution finite-element structural equations.

Computability, complexity, and languages fundamentals of theoretical computer science

CERN Document Server

Davis, Martin D; Rheinboldt, Werner

1983-01-01

Computability, Complexity, and Languages: Fundamentals of Theoretical Computer Science provides an introduction to the various aspects of theoretical computer science. Theoretical computer science is the mathematical study of models of computation. This text is composed of five parts encompassing 17 chapters, and begins with an introduction to the use of proofs in mathematics and the development of computability theory in the context of an extremely simple abstract programming language. The succeeding parts demonstrate the performance of abstract programming language using a macro expa

Bourbaki's structure theory in the problem of complex systems simulation models synthesis and model-oriented programming

Science.gov (United States)

Brodsky, Yu. I.

2015-01-01

The work is devoted to the application of Bourbaki's structure theory to substantiate the synthesis of simulation models of complex multicomponent systems, where every component may be a complex system itself. An application of the Bourbaki's structure theory offers a new approach to the design and computer implementation of simulation models of complex multicomponent systems—model synthesis and model-oriented programming. It differs from the traditional object-oriented approach. The central concept of this new approach and at the same time, the basic building block for the construction of more complex structures is the concept of models-components. A model-component endowed with a more complicated structure than, for example, the object in the object-oriented analysis. This structure provides to the model-component an independent behavior-the ability of standard responds to standard requests of its internal and external environment. At the same time, the computer implementation of model-component's behavior is invariant under the integration of models-components into complexes. This fact allows one firstly to construct fractal models of any complexity, and secondly to implement a computational process of such constructions uniformly-by a single universal program. In addition, the proposed paradigm allows one to exclude imperative programming and to generate computer code with a high degree of parallelism.

Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

Science.gov (United States)

Kassem, M.; Soize, C.; Gagliardini, L.

2009-06-01

In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

Computational structural mechanics for engine structures

Science.gov (United States)

Chamis, C. C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.

Computer analysis of the thermomechanical structure behavior. The CEASEMT system. The TEDEL code

International Nuclear Information System (INIS)

Hoffmann, A.; Jeanpierre, Francoise.

1976-01-01

TEDEL is intended for the elastoplastic computation of pipes and three-dimensional mechanical structures. Structures are described by means of jointed girder elements or more complex elements as for pipings: bended pipes, right angle elbows, tees, or any elements whose strength parameters are given to TEDEL. TEDEL is also for the dynamic computation of structures, damping included. A TEDEL option is for computing buckling critical load [fr

Modeling Cu{sup 2+}-Aβ complexes from computational approaches

Energy Technology Data Exchange (ETDEWEB)

Alí-Torres, Jorge [Departamento de Química, Universidad Nacional de Colombia- Sede Bogotá, 111321 (Colombia); Mirats, Andrea; Maréchal, Jean-Didier; Rodríguez-Santiago, Luis; Sodupe, Mariona, E-mail: Mariona.Sodupe@uab.cat [Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)

2015-09-15

Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu{sup 2+} metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu{sup 2+}-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu{sup 2+}-Aβ coordination and build plausible Cu{sup 2+}-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.

An integrative computational modelling of music structure apprehension

DEFF Research Database (Denmark)

Lartillot, Olivier

2014-01-01

, the computational model, by virtue of its generality, extensiveness and operationality, is suggested as a blueprint for the establishment of cognitively validated model of music structure apprehension. Available as a Matlab module, it can be used for practical musicological uses.......An objectivization of music analysis requires a detailed formalization of the underlying principles and methods. The formalization of the most elementary structural processes is hindered by the complexity of music, both in terms of profusions of entities (such as notes) and of tight interactions...... between a large number of dimensions. Computational modeling would enable systematic and exhaustive tests on sizeable pieces of music, yet current researches cover particular musical dimensions with limited success. The aim of this research is to conceive a computational modeling of music analysis...

Influence of the chelator structures on the stability of Re and Tc Tricarbonyl complexes: a computational study

International Nuclear Information System (INIS)

Hernández Valdés, Daniel; Rodríguez Riera, Zalua; Jáuregui Haza, Ulises; Díaz García, Alicia; Benoist, Eric

2016-01-01

The development of novel radiopharmaceuticals in nuclear medicine based on the M(CO)3 (M = Tc, Re) complexes has attracted great attention1. The versatility of this core and the easy production of the fac-[M(CO)3(H 2 O) 3 ]+ precursor could explain this interest2,3. The main characteristics of these tricarbonyl complexes are a high substitution stability of the three CO ligands and a corresponding lability of the coordinated water molecules, yielding, via easy exchange of a variety of mono-, bi-, and tridentate ligands, complexes of very high kinetic stability. A computational study of different tricarbonyl complexes for Re(I) and Tc(I) has been performed using density functional theory. The solvent effect was simulated using the polarizable continuum model. The fully optimized complexes show geometries that compare favorably with the X-ray data. These structures were used as a starting point to investigate the relative stability of tricarbonyl complexes with various tridentate ligands. They comprise an iminodiacetic acid unit for tridentate coordination to the fac-[M(CO) 3 ]+ moiety (M = Re, Tc), an aromatic ring system bearing a functional group (NO 2 -, NH 2 - and Cl-) as linking site model, and a tethering moiety (methylene, ethylene, propylene butylene or pentylene bridge) between the linking and coordinating sites. In general, Re complexes are more stables than the corresponding Tc complexes. Furthermore, the NH2 functional group, medium length in the carbon chain and meta substitution increase the stability of the complexes. The correlation of these results with the available experimental4 data on these systems allows bringing some understanding of the chemistry of tricarbonyl complexes. (author)

Unified Computational Intelligence for Complex Systems

CERN Document Server

Seiffertt, John

2010-01-01

Computational intelligence encompasses a wide variety of techniques that allow computation to learn, to adapt, and to seek. That is, they may be designed to learn information without explicit programming regarding the nature of the content to be retained, they may be imbued with the functionality to adapt to maintain their course within a complex and unpredictably changing environment, and they may help us seek out truths about our own dynamics and lives through their inclusion in complex system modeling. These capabilities place our ability to compute in a category apart from our ability to e

On the complexity of computing two nonlinearity measures

DEFF Research Database (Denmark)

Find, Magnus Gausdal

2014-01-01

We study the computational complexity of two Boolean nonlinearity measures: the nonlinearity and the multiplicative complexity. We show that if one-way functions exist, no algorithm can compute the multiplicative complexity in time 2O(n) given the truth table of length 2n, in fact under the same ...

Uncertainty Quantification for Complex RF-structures Using the State-space Concatenation Approach

CERN Document Server

Heller, Johann; Schmidt, Christian; Van Rienen, Ursula

2015-01-01

as well as to employ robust optimizations, a so-called uncertainty quantification (UQ) is applied. For large and complex structures such computations are heavily demanding and cannot be carried out using standard brute-force approaches. In this paper, we propose a combination of established techniques to perform UQ for long and complex structures, where the uncertainty is located only in parts of the structure. As exemplary structure, we investigate the third-harmonic cavity, which is being used at the FLASH accelerator at DESY, assuming an uncertain...

Computational Complexity and Human Decision-Making.

Science.gov (United States)

Bossaerts, Peter; Murawski, Carsten

2017-12-01

The rationality principle postulates that decision-makers always choose the best action available to them. It underlies most modern theories of decision-making. The principle does not take into account the difficulty of finding the best option. Here, we propose that computational complexity theory (CCT) provides a framework for defining and quantifying the difficulty of decisions. We review evidence showing that human decision-making is affected by computational complexity. Building on this evidence, we argue that most models of decision-making, and metacognition, are intractable from a computational perspective. To be plausible, future theories of decision-making will need to take into account both the resources required for implementing the computations implied by the theory, and the resource constraints imposed on the decision-maker by biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computational complexity of the landscape II-Cosmological considerations

Science.gov (United States)

Denef, Frederik; Douglas, Michael R.; Greene, Brian; Zukowski, Claire

2018-05-01

We propose a new approach for multiverse analysis based on computational complexity, which leads to a new family of "computational" measure factors. By defining a cosmology as a space-time containing a vacuum with specified properties (for example small cosmological constant) together with rules for how time evolution will produce the vacuum, we can associate global time in a multiverse with clock time on a supercomputer which simulates it. We argue for a principle of "limited computational complexity" governing early universe dynamics as simulated by this supercomputer, which translates to a global measure for regulating the infinities of eternal inflation. The rules for time evolution can be thought of as a search algorithm, whose details should be constrained by a stronger principle of "minimal computational complexity". Unlike previously studied global measures, ours avoids standard equilibrium considerations and the well-known problems of Boltzmann Brains and the youngness paradox. We also give various definitions of the computational complexity of a cosmology, and argue that there are only a few natural complexity classes.

Determining Complex Structures using Docking Method with Single Particle Scattering Data

Directory of Open Access Journals (Sweden)

Haiguang Liu

2017-04-01

Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

High-performance computing in accelerating structure design and analysis

International Nuclear Information System (INIS)

Li Zenghai; Folwell, Nathan; Ge Lixin; Guetz, Adam; Ivanov, Valentin; Kowalski, Marc; Lee, Lie-Quan; Ng, Cho-Kuen; Schussman, Greg; Stingelin, Lukas; Uplenchwar, Ravindra; Wolf, Michael; Xiao, Liling; Ko, Kwok

2006-01-01

Future high-energy accelerators such as the Next Linear Collider (NLC) will accelerate multi-bunch beams of high current and low emittance to obtain high luminosity, which put stringent requirements on the accelerating structures for efficiency and beam stability. While numerical modeling has been quite standard in accelerator R and D, designing the NLC accelerating structure required a new simulation capability because of the geometric complexity and level of accuracy involved. Under the US DOE Advanced Computing initiatives (first the Grand Challenge and now SciDAC), SLAC has developed a suite of electromagnetic codes based on unstructured grids and utilizing high-performance computing to provide an advanced tool for modeling structures at accuracies and scales previously not possible. This paper will discuss the code development and computational science research (e.g. domain decomposition, scalable eigensolvers, adaptive mesh refinement) that have enabled the large-scale simulations needed for meeting the computational challenges posed by the NLC as well as projects such as the PEP-II and RIA. Numerical results will be presented to show how high-performance computing has made a qualitative improvement in accelerator structure modeling for these accelerators, either at the component level (single cell optimization), or on the scale of an entire structure (beam heating and long-range wakefields)

Computational models of complex systems

CERN Document Server

Dabbaghian, Vahid

2014-01-01

Computational and mathematical models provide us with the opportunities to investigate the complexities of real world problems. They allow us to apply our best analytical methods to define problems in a clearly mathematical manner and exhaustively test our solutions before committing expensive resources. This is made possible by assuming parameter(s) in a bounded environment, allowing for controllable experimentation, not always possible in live scenarios. For example, simulation of computational models allows the testing of theories in a manner that is both fundamentally deductive and experimental in nature. The main ingredients for such research ideas come from multiple disciplines and the importance of interdisciplinary research is well recognized by the scientific community. This book provides a window to the novel endeavours of the research communities to present their works by highlighting the value of computational modelling as a research tool when investigating complex systems. We hope that the reader...

Large-scale computing techniques for complex system simulations

CERN Document Server

Dubitzky, Werner; Schott, Bernard

2012-01-01

Complex systems modeling and simulation approaches are being adopted in a growing number of sectors, including finance, economics, biology, astronomy, and many more. Technologies ranging from distributed computing to specialized hardware are explored and developed to address the computational requirements arising in complex systems simulations. The aim of this book is to present a representative overview of contemporary large-scale computing technologies in the context of complex systems simulations applications. The intention is to identify new research directions in this field and

Computing handbook computer science and software engineering

CERN Document Server

Gonzalez, Teofilo; Tucker, Allen

2014-01-01

Overview of Computer Science Structure and Organization of Computing Peter J. DenningComputational Thinking Valerie BarrAlgorithms and Complexity Data Structures Mark WeissBasic Techniques for Design and Analysis of Algorithms Edward ReingoldGraph and Network Algorithms Samir Khuller and Balaji RaghavachariComputational Geometry Marc van KreveldComplexity Theory Eric Allender, Michael Loui, and Kenneth ReganFormal Models and Computability Tao Jiang, Ming Li, and Bala

ANCON: A code for the evaluation of complex fault trees in personal computers

International Nuclear Information System (INIS)

Napoles, J.G.; Salomon, J.; Rivero, J.

1990-01-01

Performing probabilistic safety analysis has been recognized worldwide as one of the more effective ways for further enhancing safety of Nuclear Power Plants. The evaluation of fault trees plays a fundamental role in these analysis. Some existing limitations in RAM and execution speed of personal computers (PC) has restricted so far their use in the analysis of complex fault trees. Starting from new approaches in the data structure and other possibilities the ANCON code can evaluate complex fault trees in a PC, allowing the user to do a more comprehensive analysis of the considered system in reduced computing time

Implicit computational complexity and compilers

DEFF Research Database (Denmark)

Rubiano, Thomas

Complexity theory helps us predict and control resources, usually time and space, consumed by programs. Static analysis on specific syntactic criterion allows us to categorize some programs. A common approach is to observe the program’s data’s behavior. For instance, the detection of non...... evolution and a lot of research came from this theory. Until now, these implicit complexity theories were essentially applied on more or less toy languages. This thesis applies implicit computational complexity methods into “real life” programs by manipulating intermediate representation languages...

Computations, Complexity, Experiments, and the World Outside Physics

International Nuclear Information System (INIS)

Kadanoff, L.P

2009-01-01

Computer Models in the Sciences and Social Sciences. 1. Simulation and Prediction in Complex Systems: the Good the Bad and the Awful. This lecture deals with the history of large-scale computer modeling mostly in the context of the U.S. Department of Energy's sponsorship of modeling for weapons development and innovation in energy sources. 2. Complexity: Making a Splash-Breaking a Neck - The Making of Complexity in Physical System. For ages thinkers have been asking how complexity arise. The laws of physics are very simple. How come we are so complex? This lecture tries to approach this question by asking how complexity arises in physical fluids. 3. Forrester, et. al. Social and Biological Model-Making The partial collapse of the world's economy has raised the question of whether we could improve the performance of economic and social systems by a major effort on creating understanding via large-scale computer models. (author)

Nonlinear optical and G-Quadruplex DNA stabilization properties of novel mixed ligand copper(II) complexes and coordination polymers: Synthesis, structural characterization and computational studies

Science.gov (United States)

Rajasekhar, Bathula; Bodavarapu, Navya; Sridevi, M.; Thamizhselvi, G.; RizhaNazar, K.; Padmanaban, R.; Swu, Toka

2018-03-01

The present study reports the synthesis and evaluation of nonlinear optical property and G-Quadruplex DNA Stabilization of five novel copper(II) mixed ligand complexes. They were synthesized from copper(II) salt, 2,5- and 2,3- pyridinedicarboxylic acid, diethylenetriamine and amide based ligand (AL). The crystal structure of these complexes were determined through X-ray diffraction and supported by ESI-MAS, NMR, UV-Vis and FT-IR spectroscopic methods. Their nonlinear optical property was studied using Gaussian09 computer program. For structural optimization and nonlinear optical property, density functional theory (DFT) based B3LYP method was used with LANL2DZ basis set for metal ion and 6-31G∗ for C,H,N,O and Cl atoms. The present work reveals that pre-polarized Complex-2 showed higher β value (29.59 × 10-30e.s.u) as compared to that of neutral complex-1 (β = 0.276 × 10-30e.s.u.) which may be due to greater advantage of polarizability. Complex-2 is expected to be a potential material for optoelectronic and photonic technologies. Docking studies using AutodockVina revealed that complex-2 has higher binding energy for both G-Quadruplex DNA (-8.7 kcal/mol) and duplex DNA (-10.1 kcal/mol). It was also observed that structure plays an important role in binding efficiency.

Introduction to the LaRC central scientific computing complex

Science.gov (United States)

Shoosmith, John N.

1993-01-01

The computers and associated equipment that make up the Central Scientific Computing Complex of the Langley Research Center are briefly described. The electronic networks that provide access to the various components of the complex and a number of areas that can be used by Langley and contractors staff for special applications (scientific visualization, image processing, software engineering, and grid generation) are also described. Flight simulation facilities that use the central computers are described. Management of the complex, procedures for its use, and available services and resources are discussed. This document is intended for new users of the complex, for current users who wish to keep appraised of changes, and for visitors who need to understand the role of central scientific computers at Langley.

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

Science.gov (United States)

Subramaniam, Karthigeyan

2016-08-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and processes in social settings like classrooms thereby providing glimpses into the complex dynamics of teacher-students interactions, configurations, and conventions during collective meaning making and knowledge creation. Data included observations, interviews, and focus group interviews. Analysis revealed that the dominant participation structure evident within participants' instruction with computer technology was ( Teacher) initiation-( Student and Teacher) response sequences-( Teacher) evaluate participation structure. Three key events characterized the how participants organized this participation structure in their classrooms: setting the stage for interactive instruction, the joint activity, and maintaining accountability. Implications include the following: (1) teacher educators need to tap into the knowledge base that underscores science teachers' learning to teach philosophies when computer technology is used in instruction. (2) Teacher educators need to emphasize the essential idea that learning and cognition is not situated within the computer technology but within the pedagogical practices, specifically the participation structures. (3) The pedagogical practices developed with the integration or with the use of computer technology underscored by the teachers' own knowledge of classroom contexts and curriculum needs to be the focus for how students learn science content with computer technology instead of just focusing on how computer technology solely supports students learning of science content.

Algebraic computability and enumeration models recursion theory and descriptive complexity

CERN Document Server

Nourani, Cyrus F

2016-01-01

This book, Algebraic Computability and Enumeration Models: Recursion Theory and Descriptive Complexity, presents new techniques with functorial models to address important areas on pure mathematics and computability theory from the algebraic viewpoint. The reader is first introduced to categories and functorial models, with Kleene algebra examples for languages. Functorial models for Peano arithmetic are described toward important computational complexity areas on a Hilbert program, leading to computability with initial models. Infinite language categories are also introduced to explain descriptive complexity with recursive computability with admissible sets and urelements. Algebraic and categorical realizability is staged on several levels, addressing new computability questions with omitting types realizably. Further applications to computing with ultrafilters on sets and Turing degree computability are examined. Functorial models computability is presented with algebraic trees realizing intuitionistic type...

Complex DNA structures and structures of DNA complexes

International Nuclear Information System (INIS)

Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J.

1994-01-01

Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe 1 H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful

Complex DNA structures and structures of DNA complexes

Energy Technology Data Exchange (ETDEWEB)

Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J. [Scripps Research Institute, La Jolla, CA (United States)

1994-12-01

Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

3D complex: a structural classification of protein complexes.

Directory of Open Access Journals (Sweden)

Emmanuel D Levy

2006-11-01

Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

Structural Information Inference from Lanthanoid Complexing Systems: Photoluminescence Studies on Isolated Ions

Science.gov (United States)

Greisch, Jean Francois; Harding, Michael E.; Chmela, Jiri; Klopper, Willem M.; Schooss, Detlef; Kappes, Manfred M.

2016-06-01

The application of lanthanoid complexes ranges from photovoltaics and light-emitting diodes to quantum memories and biological assays. Rationalization of their design requires a thorough understanding of intramolecular processes such as energy transfer, charge transfer, and non-radiative decay involving their subunits. Characterization of the excited states of such complexes considerably benefits from mass spectrometric methods since the associated optical transitions and processes are strongly affected by stoichiometry, symmetry, and overall charge state. We report herein spectroscopic measurements on ensembles of ions trapped in the gas phase and soft-landed in neon matrices. Their interpretation is considerably facilitated by direct comparison with computations. The combination of energy- and time-resolved measurements on isolated species with density functional as well as ligand-field and Franck-Condon computations enables us to infer structural as well as dynamical information about the species studied. The approach is first illustrated for sets of model lanthanoid complexes whose structure and electronic properties are systematically varied via the substitution of one component (lanthanoid or alkali,alkali-earth ion): (i) systematic dependence of ligand-centered phosphorescence on the lanthanoid(III) promotion energy and its impact on sensitization, and (ii) structural changes induced by the substitution of alkali or alkali-earth ions in relation with structures inferred using ion mobility spectroscopy. The temperature dependence of sensitization is briefly discussed. The focus is then shifted to measurements involving europium complexes with doxycycline an antibiotic of the tetracycline family. Besides discussing the complexes' structural and electronic features, we report on their use to monitor enzymatic processes involving hydrogen peroxide or biologically relevant molecules such as adenosine triphosphate (ATP).

Structured analysis and modeling of complex systems

Science.gov (United States)

Strome, David R.; Dalrymple, Mathieu A.

1992-01-01

The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

Automated analysis and design of complex structures

International Nuclear Information System (INIS)

Wilson, E.L.

1977-01-01

The present application of optimum design appears to be restricted to components of the structure rather than to the total structural system. Since design normally involved many analysis of the system any improvement in the efficiency of the basic methods of analysis will allow more complicated systems to be designed by optimum methods. The evaluation of the risk and reliability of a structural system can be extremely important. Reliability studies have been made of many non-structural systems for which the individual components have been extensively tested and the service environment is known. For such systems the reliability studies are valid. For most structural systems, however, the properties of the components can only be estimated and statistical data associated with the potential loads is often minimum. Also, a potentially critical loading condition may be completely neglected in the study. For these reasons and the previous problems associated with the reliability of both linear and nonlinear analysis computer programs it appears to be premature to place a significant value on such studies for complex structures. With these comments as background the purpose of this paper is to discuss the following: the relationship of analysis to design; new methods of analysis; new of improved finite elements; effect of minicomputer on structural analysis methods; the use of system of microprocessors for nonlinear structural analysis; the role of interacting graphics systems in future analysis and design. This discussion will focus on the impact of new, inexpensive computer hardware on design and analysis methods

Computer graphics in piping structural engineering

International Nuclear Information System (INIS)

Revesz, Z.

1985-01-01

Computer graphics in piping structural engineering is gaining in popularity. The large number of systems, the growing complexity of the load cases and structure models require human assimilation of large amounts of data. An effort has been made to enlighten evaluation of numerical data and visualize as much of it as possible, thus eliminating a source of error and accelerating analysis/reporting. The product of this effort is PAID, the Piping Analysis and Interactive Design software. While developing PAID, interest has been focused on the acceleration of the work done mainly by PIPESTRESS. Some installed and tested capabilities of PAID are presented in this paper. Examples are given from the graphic output in report form and the conversation necessary to get such is demonstrated. (orig.)

Polyacrylic acids–bovine serum albumin complexation: Structure and dynamics

International Nuclear Information System (INIS)

Othman, Mohamed; Aschi, Adel; Gharbi, Abdelhafidh

2016-01-01

The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH. - Highlights: • Influence of physico-chemical parameters on the electrostatic interactions in the complex system (polyelectrolyte/protein). • Stabilization and encapsulation of biological macromolecules solution by mean of polyelectrolyte. • Properties and structure of mixture obtained by screening the charges of globular protein and at different masses of polyacrylic acids. • Dynamic of the constituents formed by complexes particles. • Evaluation of the electrostatic properties of bovine serum albumin versus pH through solution of the Poisson-Boltzmann equation.

Ubiquitous Computing, Complexity and Culture

DEFF Research Database (Denmark)

environments, experience time, and develop identities individually and socially. Interviews with working media artists lend further perspectives on these cultural transformations. Drawing on cultural theory, new media art studies, human-computer interaction theory, and software studies, this cutting-edge book......The ubiquitous nature of mobile and pervasive computing has begun to reshape and complicate our notions of space, time, and identity. In this collection, over thirty internationally recognized contributors reflect on ubiquitous computing’s implications for the ways in which we interact with our...... critically unpacks the complex ubiquity-effects confronting us every day....

Computation of the Complex Probability Function

Energy Technology Data Exchange (ETDEWEB)

Trainer, Amelia Jo [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ledwith, Patrick John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-08-22

The complex probability function is important in many areas of physics and many techniques have been developed in an attempt to compute it for some z quickly and e ciently. Most prominent are the methods that use Gauss-Hermite quadrature, which uses the roots of the n^th degree Hermite polynomial and corresponding weights to approximate the complex probability function. This document serves as an overview and discussion of the use, shortcomings, and potential improvements on the Gauss-Hermite quadrature for the complex probability function.

Software Accelerates Computing Time for Complex Math

Science.gov (United States)

2014-01-01

Ames Research Center awarded Newark, Delaware-based EM Photonics Inc. SBIR funding to utilize graphic processing unit (GPU) technology- traditionally used for computer video games-to develop high-computing software called CULA. The software gives users the ability to run complex algorithms on personal computers with greater speed. As a result of the NASA collaboration, the number of employees at the company has increased 10 percent.

Advances in computational dynamics of particles, materials and structures a unified approach

CERN Document Server

Har, Jason

2012-01-01

Computational methods for the modeling and simulation of the dynamic response and behavior of particles, materials and structural systems have had a profound influence on science, engineering and technology. Complex science and engineering applications dealing with complicated structural geometries and materials that would be very difficult to treat using analytical methods have been successfully simulated using computational tools. With the incorporation of quantum, molecular and biological mechanics into new models, these methods are poised to play an even bigger role in the future. Ad

Applications of Computer Technology in Complex Craniofacial Reconstruction

Directory of Open Access Journals (Sweden)

Kristopher M. Day, MD

2018-03-01

Conclusion:. Modern 3D technology allows the surgeon to better analyze complex craniofacial deformities, precisely plan surgical correction with computer simulation of results, customize osteotomies, plan distractions, and print 3DPCI, as needed. The use of advanced 3D computer technology can be applied safely and potentially improve aesthetic and functional outcomes after complex craniofacial reconstruction. These techniques warrant further study and may be reproducible in various centers of care.

Three-Dimensional Numerical Analysis of Compound Lining in Complex Underground Surge-Shaft Structure

Directory of Open Access Journals (Sweden)

Juntao Chen

2015-01-01

Full Text Available The mechanical behavior of lining structure of deep-embedded cylinder surge shaft with multifork tunnel is analyzed using three-dimensional nonlinear FEM. With the elastic-plastic constitutive relations of rock mass imported and the implicit bolt element and distributed concrete cracking model adopted, a computing method of complex surge shaft is presented for the simulation of underground excavations and concrete lining cracks. In order to reflect the interaction and initial gap between rock mass and concrete lining, a three-dimensional nonlinear interface element is adopted, which can take into account both the normal and tangential characteristics. By an actual engineering computation, the distortion characteristics and stress distribution rules of the dimensional multifork surge-shaft lining structure under different behavior are revealed. The results verify the rationality and feasibility of this computation model and method and provide a new idea and reference for the complex surge-shaft design and construction.

Computational Modeling of Complex Protein Activity Networks

NARCIS (Netherlands)

Schivo, Stefano; Leijten, Jeroen; Karperien, Marcel; Post, Janine N.; Prignet, Claude

2017-01-01

Because of the numerous entities interacting, the complexity of the networks that regulate cell fate makes it impossible to analyze and understand them using the human brain alone. Computational modeling is a powerful method to unravel complex systems. We recently described the development of a

Computational intelligence methods for the efficient reliability analysis of complex flood defence structures

NARCIS (Netherlands)

Kingston, Greer B.; Rajabali Nejad, Mohammadreza; Gouldby, Ben P.; van Gelder, Pieter H.A.J.M.

2011-01-01

With the continual rise of sea levels and deterioration of flood defence structures over time, it is no longer appropriate to define a design level of flood protection, but rather, it is necessary to estimate the reliability of flood defences under varying and uncertain conditions. For complex

Blind trials of computer-assisted structure elucidation software

Directory of Open Access Journals (Sweden)

Moser Arvin

2012-02-01

Full Text Available Abstract Background One of the largest challenges in chemistry today remains that of efficiently mining through vast amounts of data in order to elucidate the chemical structure for an unknown compound. The elucidated candidate compound must be fully consistent with the data and any other competing candidates efficiently eliminated without doubt by using additional data if necessary. It has become increasingly necessary to incorporate an in silico structure generation and verification tool to facilitate this elucidation process. An effective structure elucidation software technology aims to mimic the skills of a human in interpreting the complex nature of spectral data while producing a solution within a reasonable amount of time. This type of software is known as computer-assisted structure elucidation or CASE software. A systematic trial of the ACD/Structure Elucidator CASE software was conducted over an extended period of time by analysing a set of single and double-blind trials submitted by a global audience of scientists. The purpose of the blind trials was to reduce subjective bias. Double-blind trials comprised of data where the candidate compound was unknown to both the submitting scientist and the analyst. The level of expertise of the submitting scientist ranged from novice to expert structure elucidation specialists with experience in pharmaceutical, industrial, government and academic environments. Results Beginning in 2003, and for the following nine years, the algorithms and software technology contained within ACD/Structure Elucidator have been tested against 112 data sets; many of these were unique challenges. Of these challenges 9% were double-blind trials. The results of eighteen of the single-blind trials were investigated in detail and included problems of a diverse nature with many of the specific challenges associated with algorithmic structure elucidation such as deficiency in protons, structure symmetry, a large number of

The structure of complex Lie groups

CERN Document Server

Lee, Dong Hoon

2001-01-01

Complex Lie groups have often been used as auxiliaries in the study of real Lie groups in areas such as differential geometry and representation theory. To date, however, no book has fully explored and developed their structural aspects.The Structure of Complex Lie Groups addresses this need. Self-contained, it begins with general concepts introduced via an almost complex structure on a real Lie group. It then moves to the theory of representative functions of Lie groups- used as a primary tool in subsequent chapters-and discusses the extension problem of representations that is essential for studying the structure of complex Lie groups. This is followed by a discourse on complex analytic groups that carry the structure of affine algebraic groups compatible with their analytic group structure. The author then uses the results of his earlier discussions to determine the observability of subgroups of complex Lie groups.The differences between complex algebraic groups and complex Lie groups are sometimes subtle ...

Data structures, computer graphics, and pattern recognition

CERN Document Server

Klinger, A; Kunii, T L

1977-01-01

Data Structures, Computer Graphics, and Pattern Recognition focuses on the computer graphics and pattern recognition applications of data structures methodology.This book presents design related principles and research aspects of the computer graphics, system design, data management, and pattern recognition tasks. The topics include the data structure design, concise structuring of geometric data for computer aided design, and data structures for pattern recognition algorithms. The survey of data structures for computer graphics systems, application of relational data structures in computer gr

Metasynthetic computing and engineering of complex systems

CERN Document Server

Cao, Longbing

2015-01-01

Provides a comprehensive overview and introduction to the concepts, methodologies, analysis, design and applications of metasynthetic computing and engineering. The author: Presents an overview of complex systems, especially open complex giant systems such as the Internet, complex behavioural and social problems, and actionable knowledge discovery and delivery in the big data era. Discusses ubiquitous intelligence in complex systems, including human intelligence, domain intelligence, social intelligence, network intelligence, data intelligence and machine intelligence, and their synergy thro

Computability, complexity, logic

CERN Document Server

Börger, Egon

1989-01-01

The theme of this book is formed by a pair of concepts: the concept of formal language as carrier of the precise expression of meaning, facts and problems, and the concept of algorithm or calculus, i.e. a formally operating procedure for the solution of precisely described questions and problems. The book is a unified introduction to the modern theory of these concepts, to the way in which they developed first in mathematical logic and computability theory and later in automata theory, and to the theory of formal languages and complexity theory. Apart from considering the fundamental themes an

RADCHARM++: A C++ routine to compute the electromagnetic radiation generated by relativistic charged particles in crystals and complex structures

Energy Technology Data Exchange (ETDEWEB)

Bandiera, Laura; Bagli, Enrico; Guidi, Vincenzo [INFN Sezione di Ferrara and Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Ferrara, Via Saragat 1, 44121 Ferrara (Italy); Tikhomirov, Victor V. [Research Institute for Nuclear Problems, Belarusian State University, Minsk (Belarus)

2015-07-15

The analytical theories of coherent bremsstrahlung and channeling radiation well describe the process of radiation generation in crystals under some special cases. However, the treatment of complex situations requires the usage of a more general approach. In this report we present a C++ routine, named RADCHARM++, to compute the electromagnetic radiation emitted by electrons and positrons in crystals and complex structures. In the RADCHARM++ routine, the model for the computation of e.m. radiation generation is based on the direct integration of the quasiclassical formula of Baier and Katkov. This approach allows one taking into account real trajectories, and thereby the contribution of incoherent scattering. Such contribution can be very important in many cases, for instance for electron channeling. The generality of the Baier–Katkov operator method permits one to simulate the electromagnetic radiation emitted by electrons/positrons in very different cases, e.g., in straight, bent and periodically bent crystals, and for different beam energy ranges, from sub-GeV to TeV and above. The RADCHARM++ routine has been implemented in the Monte Carlo code DYNECHARM++, which solves the classical equation of motion of charged particles traveling through a crystal under the continuum potential approximation. The code has proved to reproduce the results of experiments performed at the MAinzer MIkrotron (MAMI) with 855 MeV electrons and has been used to predict the radiation spectrum generated by the same electron beam in a bent crystal.

Coherence and computational complexity of quantifier-free dependence logic formulas

NARCIS (Netherlands)

Kontinen, J.; Kontinen, J.; Väänänen, J.

2010-01-01

We study the computational complexity of the model checking for quantifier-free dependence logic (D) formulas. We point out three thresholds in the computational complexity: logarithmic space, non- deterministic logarithmic space and non-deterministic polynomial time.

Discrete computational structures

CERN Document Server

Korfhage, Robert R

1974-01-01

Discrete Computational Structures describes discrete mathematical concepts that are important to computing, covering necessary mathematical fundamentals, computer representation of sets, graph theory, storage minimization, and bandwidth. The book also explains conceptual framework (Gorn trees, searching, subroutines) and directed graphs (flowcharts, critical paths, information network). The text discusses algebra particularly as it applies to concentrates on semigroups, groups, lattices, propositional calculus, including a new tabular method of Boolean function minimization. The text emphasize

Achievements and challenges in structural bioinformatics and computational biophysics.

Science.gov (United States)

Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

2015-01-01

The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

Structure problems in the analog computation

International Nuclear Information System (INIS)

Braffort, P.L.

1957-01-01

The recent mathematical development showed the importance of elementary structures (algebraic, topological, etc.) in abeyance under the great domains of classical analysis. Such structures in analog computation are put in evidence and possible development of applied mathematics are discussed. It also studied the topological structures of the standard representation of analog schemes such as additional triangles, integrators, phase inverters and functions generators. The analog method gives only the function of the variable: time, as results of its computations. But the course of computation, for systems including reactive circuits, introduces order structures which are called 'chronological'. Finally, it showed that the approximation methods of ordinary numerical and digital computation present the same structure as these analog computation. The structure analysis permits fruitful comparisons between the several domains of applied mathematics and suggests new important domains of application for analog method. (M.P.)

The spectra of type IIB flux compactifications at large complex structure

International Nuclear Information System (INIS)

Brodie, Callum; Marsh, M.C. David

2016-01-01

We compute the spectra of the Hessian matrix, H, and the matrix M that governs the critical point equation of the low-energy effective supergravity, as a function of the complex structure and axio-dilaton moduli space in type IIB flux compactifications at large complex structure. We find both spectra analytically in an h − 1,2 +3 real-dimensional subspace of the moduli space, and show that they exhibit a universal structure with highly degenerate eigenvalues, independently of the choice of flux, the details of the compactification geometry, and the number of complex structure moduli. In this subspace, the spectrum of the Hessian matrix contains no tachyons, but there are also no critical points. We show numerically that the spectra of H and M remain highly peaked over a large fraction of the sampled moduli space of explicit Calabi-Yau compactifications with 2 to 5 complex structure moduli. In these models, the scale of the supersymmetric contribution to the scalar masses is strongly linearly correlated with the value of the superpotential over almost the entire moduli space, with particularly strong correlations arising for g s <1. We contrast these results with the expectations from the much-used continuous flux approximation, and comment on the applicability of Random Matrix Theory to the statistical modelling of the string theory landscape.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

KAUST Repository

Guturu, H.

2013-11-11

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and \\'through-DNA\\' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

KAUST Repository

Guturu, H.; Doxey, A. C.; Wenger, A. M.; Bejerano, G.

2013-01-01

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and 'through-DNA' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Computational model of dose response for low-LET-induced complex chromosomal aberrations

International Nuclear Information System (INIS)

Eidelman, Y.A.; Andreev, S.G.

2015-01-01

Experiments with full-colour mFISH chromosome painting have revealed high yield of radiation-induced complex chromosomal aberrations (CAs). The ratio of complex to simple aberrations is dependent on cell type and linear energy transfer. Theoretical analysis has demonstrated that the mechanism of CA formation as a result of interaction between lesions at a surface of chromosome territories does not explain high complexes-to-simples ratio in human lymphocytes. The possible origin of high yields of γ-induced complex CAs was investigated in the present work by computer simulation. CAs were studied on the basis of chromosome structure and dynamics modelling and the hypothesis of CA formation on nuclear centres. The spatial organisation of all chromosomes in a human interphase nucleus was predicted by simulation of mitosis-to-interphase chromosome structure transition. Two scenarios of CA formation were analysed, 'static' (existing in a nucleus prior to irradiation) centres and 'dynamic' (formed in response to irradiation) centres. The modelling results reveal that under certain conditions, both scenarios explain quantitatively the dose-response relationships for both simple and complex γ-induced inter-chromosomal exchanges observed by mFISH chromosome painting in the first post-irradiation mitosis in human lymphocytes. (authors)

Interactive computer graphics and its role in control system design of large space structures

Science.gov (United States)

Reddy, A. S. S. R.

1985-01-01

This paper attempts to show the relevance of interactive computer graphics in the design of control systems to maintain attitude and shape of large space structures to accomplish the required mission objectives. The typical phases of control system design, starting from the physical model such as modeling the dynamics, modal analysis, and control system design methodology are reviewed and the need of the interactive computer graphics is demonstrated. Typical constituent parts of large space structures such as free-free beams and free-free plates are used to demonstrate the complexity of the control system design and the effectiveness of the interactive computer graphics.

Molecular computing towards a novel computing architecture for complex problem solving

CERN Document Server

Chang, Weng-Long

2014-01-01

This textbook introduces a concise approach to the design of molecular algorithms for students or researchers who are interested in dealing with complex problems. Through numerous examples and exercises, you will understand the main difference of molecular circuits and traditional digital circuits to manipulate the same problem and you will also learn how to design a molecular algorithm of solving any a problem from start to finish. The book starts with an introduction to computational aspects of digital computers and molecular computing, data representation of molecular computing, molecular operations of molecular computing and number representation of molecular computing, and provides many molecular algorithm to construct the parity generator and the parity checker of error-detection codes on digital communication, to encode integers of different formats, single precision and double precision of floating-point numbers, to implement addition and subtraction of unsigned integers, to construct logic operations...

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

Energy Technology Data Exchange (ETDEWEB)

Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

2014-06-01

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

Structure-based characterization of multiprotein complexes.

Science.gov (United States)

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Computer Simulations and Theoretical Studies of Complex Systems: from complex fluids to frustrated magnets

Science.gov (United States)

Choi, Eunsong

Computer simulations are an integral part of research in modern condensed matter physics; they serve as a direct bridge between theory and experiment by systemactically applying a microscopic model to a collection of particles that effectively imitate a macroscopic system. In this thesis, we study two very differnt condensed systems, namely complex fluids and frustrated magnets, primarily by simulating classical dynamics of each system. In the first part of the thesis, we focus on ionic liquids (ILs) and polymers--the two complementary classes of materials that can be combined to provide various unique properties. The properties of polymers/ILs systems, such as conductivity, viscosity, and miscibility, can be fine tuned by choosing an appropriate combination of cations, anions, and polymers. However, designing a system that meets a specific need requires a concrete understanding of physics and chemistry that dictates a complex interplay between polymers and ionic liquids. In this regard, molecular dynamics (MD) simulation is an efficient tool that provides a molecular level picture of such complex systems. We study the behavior of Poly (ethylene oxide) (PEO) and the imidazolium based ionic liquids, using MD simulations and statistical mechanics. We also discuss our efforts to develop reliable and efficient classical force-fields for PEO and the ionic liquids. The second part is devoted to studies on geometrically frustrated magnets. In particular, a microscopic model, which gives rise to an incommensurate spiral magnetic ordering observed in a pyrochlore antiferromagnet is investigated. The validation of the model is made via a comparison of the spin-wave spectra with the neutron scattering data. Since the standard Holstein-Primakoff method is difficult to employ in such a complex ground state structure with a large unit cell, we carry out classical spin dynamics simulations to compute spin-wave spectra directly from the Fourier transform of spin trajectories. We

Reduced-order computational model in nonlinear structural dynamics for structures having numerous local elastic modes in the low-frequency range. Application to fuel assemblies

International Nuclear Information System (INIS)

Batou, A.; Soize, C.; Brie, N.

2013-01-01

Highlights: • A ROM of a nonlinear dynamical structure is built with a global displacements basis. • The reduced order model of fuel assemblies is accurate and of very small size. • The shocks between grids of a row of seven fuel assemblies are computed. -- Abstract: We are interested in the construction of a reduced-order computational model for nonlinear complex dynamical structures which are characterized by the presence of numerous local elastic modes in the low-frequency band. This high modal density makes the use of the classical modal analysis method not suitable. Therefore the reduced-order computational model is constructed using a basis of a space of global displacements, which is constructed a priori and which allows the nonlinear dynamical response of the structure observed on the stiff part to be predicted with a good accuracy. The methodology is applied to a complex industrial structure which is made up of a row of seven fuel assemblies with possibility of collisions between grids and which is submitted to a seismic loading

Reduced-order computational model in nonlinear structural dynamics for structures having numerous local elastic modes in the low-frequency range. Application to fuel assemblies

Energy Technology Data Exchange (ETDEWEB)

Batou, A., E-mail: anas.batou@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France); Soize, C., E-mail: christian.soize@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France); Brie, N., E-mail: nicolas.brie@edf.fr [EDF R and D, Département AMA, 1 avenue du général De Gaulle, 92140 Clamart (France)

2013-09-15

Highlights: • A ROM of a nonlinear dynamical structure is built with a global displacements basis. • The reduced order model of fuel assemblies is accurate and of very small size. • The shocks between grids of a row of seven fuel assemblies are computed. -- Abstract: We are interested in the construction of a reduced-order computational model for nonlinear complex dynamical structures which are characterized by the presence of numerous local elastic modes in the low-frequency band. This high modal density makes the use of the classical modal analysis method not suitable. Therefore the reduced-order computational model is constructed using a basis of a space of global displacements, which is constructed a priori and which allows the nonlinear dynamical response of the structure observed on the stiff part to be predicted with a good accuracy. The methodology is applied to a complex industrial structure which is made up of a row of seven fuel assemblies with possibility of collisions between grids and which is submitted to a seismic loading.

High performance parallel computing of flows in complex geometries: I. Methods

International Nuclear Information System (INIS)

Gourdain, N; Gicquel, L; Montagnac, M; Vermorel, O; Staffelbach, G; Garcia, M; Boussuge, J-F; Gazaix, M; Poinsot, T

2009-01-01

Efficient numerical tools coupled with high-performance computers, have become a key element of the design process in the fields of energy supply and transportation. However flow phenomena that occur in complex systems such as gas turbines and aircrafts are still not understood mainly because of the models that are needed. In fact, most computational fluid dynamics (CFD) predictions as found today in industry focus on a reduced or simplified version of the real system (such as a periodic sector) and are usually solved with a steady-state assumption. This paper shows how to overcome such barriers and how such a new challenge can be addressed by developing flow solvers running on high-end computing platforms, using thousands of computing cores. Parallel strategies used by modern flow solvers are discussed with particular emphases on mesh-partitioning, load balancing and communication. Two examples are used to illustrate these concepts: a multi-block structured code and an unstructured code. Parallel computing strategies used with both flow solvers are detailed and compared. This comparison indicates that mesh-partitioning and load balancing are more straightforward with unstructured grids than with multi-block structured meshes. However, the mesh-partitioning stage can be challenging for unstructured grids, mainly due to memory limitations of the newly developed massively parallel architectures. Finally, detailed investigations show that the impact of mesh-partitioning on the numerical CFD solutions, due to rounding errors and block splitting, may be of importance and should be accurately addressed before qualifying massively parallel CFD tools for a routine industrial use.

ANS main control complex three-dimensional computer model development

International Nuclear Information System (INIS)

Cleaves, J.E.; Fletcher, W.M.

1993-01-01

A three-dimensional (3-D) computer model of the Advanced Neutron Source (ANS) main control complex is being developed. The main control complex includes the main control room, the technical support center, the materials irradiation control room, computer equipment rooms, communications equipment rooms, cable-spreading rooms, and some support offices and breakroom facilities. The model will be used to provide facility designers and operations personnel with capabilities for fit-up/interference analysis, visual ''walk-throughs'' for optimizing maintain-ability, and human factors and operability analyses. It will be used to determine performance design characteristics, to generate construction drawings, and to integrate control room layout, equipment mounting, grounding equipment, electrical cabling, and utility services into ANS building designs. This paper describes the development of the initial phase of the 3-D computer model for the ANS main control complex and plans for its development and use

Automated System for Teaching Computational Complexity of Algorithms Course

Directory of Open Access Journals (Sweden)

Vadim S. Roublev

2017-01-01

Full Text Available This article describes problems of designing automated teaching system for “Computational complexity of algorithms” course. This system should provide students with means to familiarize themselves with complex mathematical apparatus and improve their mathematical thinking in the respective area. The article introduces the technique of algorithms symbol scroll table that allows estimating lower and upper bounds of computational complexity. Further, we introduce a set of theorems that facilitate the analysis in cases when the integer rounding of algorithm parameters is involved and when analyzing the complexity of a sum. At the end, the article introduces a normal system of symbol transformations that allows one both to perform any symbol transformations and simplifies the automated validation of such transformations. The article is published in the authors’ wording.

Characterizations and computational complexity of systolic trellis automata

Energy Technology Data Exchange (ETDEWEB)

Ibarra, O H; Kim, S M

1984-03-01

Systolic trellis automata are simple models for VLSI. The authors characterize the computing power of these models in terms of turing machines. The characterizations are useful in proving new results as well as giving simpler proofs of known results. They also derive lower and upper bounds on the computational complexity of the models. 18 references.

Computational and experimental analyses of the wave propagation through a bar structure including liquid-solid interface

Energy Technology Data Exchange (ETDEWEB)

Park, Sang Jin [UST Graduate School, Daejeon (Korea, Republic of); Rhee, Hui Nam [Division of Mechanical and Aerospace Engineering, Sunchon National University, Sunchon (Korea, Republic of); Yoon, Doo Byung; Park, Jin Ho [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2015-08-15

In this research, we study the propagation of longitudinal and transverse waves through a metal rod including a liquid layer using computational and experimental analyses. The propagation characteristics of longitudinal and transverse waves obtained by the computational and experimental analyses were consistent with the wave propagation theory for both cases, that is, the homogeneous metal rod and the metal rod including a liquid layer. The fluid-structure interaction modeling technique developed for the computational wave propagation analysis in this research can be applied to the more complex structures including solid-liquid interfaces.

Using computer simulations to probe the structure and dynamics of biopolymers

International Nuclear Information System (INIS)

Levy, R.M.; Hirata, F.; Kim, K.; Zhang, P.

1987-01-01

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper the authors review recent work in their laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized: (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper the authors review a more analytical approach they developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations

Computational complexity of Boolean functions

Energy Technology Data Exchange (ETDEWEB)

Korshunov, Aleksei D [Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

2012-02-28

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.

VBOT: Motivating computational and complex systems fluencies with constructionist virtual/physical robotics

Science.gov (United States)

Berland, Matthew W.

As scientists use the tools of computational and complex systems theory to broaden science perspectives (e.g., Bar-Yam, 1997; Holland, 1995; Wolfram, 2002), so can middle-school students broaden their perspectives using appropriate tools. The goals of this dissertation project are to build, study, evaluate, and compare activities designed to foster both computational and complex systems fluencies through collaborative constructionist virtual and physical robotics. In these activities, each student builds an agent (e.g., a robot-bird) that must interact with fellow students' agents to generate a complex aggregate (e.g., a flock of robot-birds) in a participatory simulation environment (Wilensky & Stroup, 1999a). In a participatory simulation, students collaborate by acting in a common space, teaching each other, and discussing content with one another. As a result, the students improve both their computational fluency and their complex systems fluency, where fluency is defined as the ability to both consume and produce relevant content (DiSessa, 2000). To date, several systems have been designed to foster computational and complex systems fluencies through computer programming and collaborative play (e.g., Hancock, 2003; Wilensky & Stroup, 1999b); this study suggests that, by supporting the relevant fluencies through collaborative play, they become mutually reinforcing. In this work, I will present both the design of the VBOT virtual/physical constructionist robotics learning environment and a comparative study of student interaction with the virtual and physical environments across four middle-school classrooms, focusing on the contrast in systems perspectives differently afforded by the two environments. In particular, I found that while performance gains were similar overall, the physical environment supported agent perspectives on aggregate behavior, and the virtual environment supported aggregate perspectives on agent behavior. The primary research questions

Structural Characterization of Am(III)- and Pu(III)-DOTA Complexes.

Science.gov (United States)

Audras, Matthieu; Berthon, Laurence; Berthon, Claude; Guillaumont, Dominique; Dumas, Thomas; Illy, Marie-Claire; Martin, Nicolas; Zilbermann, Israel; Moiseev, Yulia; Ben-Eliyahu, Yeshayahu; Bettelheim, Armand; Cammelli, Sebastiano; Hennig, Christoph; Moisy, Philippe

2017-10-16

The complexation of 1,4,7,10-tetrazacyclodecane-1,4,7,10-tetraacetic acid (DOTA) ligand with two trivalent actinides (Am 3+ and Pu 3+ ) was investigated by UV-visible spectrophotometry, NMR spectroscopy, and extended X-ray absorption fine structure in conjunction with computational methods. The complexation process of these two cations is similar to what has been previously observed with lanthanides(III) of similar ionic radius. The complexation takes place in different steps and ends with the formation of a (1:1) complex [(An(III)DOTA)(H 2 O)] - , where the cation is bonded to the nitrogen atoms of the ring, the four carboxylate arms, and a water molecule to complete the coordination sphere. The formation of An(III)-DOTA complexes is faster than the Ln(III)-DOTA systems of equivalent ionic radius. Furthermore, it is found that An-N distances are slightly shorter than Ln-N distances. Theoretical calculations showed that the slightly higher affinity of DOTA toward Am over Nd is correlated with slightly enhanced ligand-to-metal charge donation arising from oxygen and nitrogen atoms.

Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering

OpenAIRE

Karlheinz Schwarz; Rainer Breitling; Christian Allen

2013-01-01

Computation (ISSN 2079-3197; http://www.mdpi.com/journal/computation) is an international scientific open access journal focusing on fundamental work in the field of computational science and engineering. Computational science has become essential in many research areas by contributing to solving complex problems in fundamental science all the way to engineering. The very broad range of application domains suggests structuring this journal into three sections, which are briefly characterized ...

Complex band structure and electronic transmission eigenchannels

DEFF Research Database (Denmark)

Jensen, Anders; Strange, Mikkel; Smidstrup, Soren

2017-01-01

and complex band structure, in this case individual eigenchannel transmissions and different complex bands. We present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT Landauer transport calculations for one semi-conductor and two...

Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.

Science.gov (United States)

Baichoo, Shakuntala; Ouzounis, Christos A

A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. The complexity aspect is poised to become pivotal as we will be facing challenges related to the continuous increase of genomic data on unprecedented scales and complexity in the foreseeable future, when robust biological simulation at the cell level and above becomes a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

Computing complex Airy functions by numerical quadrature

NARCIS (Netherlands)

A. Gil (Amparo); J. Segura (Javier); N.M. Temme (Nico)

2001-01-01

textabstractIntegral representations are considered of solutions of the Airydifferential equation w''-z, w=0 for computing Airy functions for complex values of z.In a first method contour integral representations of the Airyfunctions are written as non-oscillating

High performance parallel computing of flows in complex geometries: II. Applications

International Nuclear Information System (INIS)

Gourdain, N; Gicquel, L; Staffelbach, G; Vermorel, O; Duchaine, F; Boussuge, J-F; Poinsot, T

2009-01-01

Present regulations in terms of pollutant emissions, noise and economical constraints, require new approaches and designs in the fields of energy supply and transportation. It is now well established that the next breakthrough will come from a better understanding of unsteady flow effects and by considering the entire system and not only isolated components. However, these aspects are still not well taken into account by the numerical approaches or understood whatever the design stage considered. The main challenge is essentially due to the computational requirements inferred by such complex systems if it is to be simulated by use of supercomputers. This paper shows how new challenges can be addressed by using parallel computing platforms for distinct elements of a more complex systems as encountered in aeronautical applications. Based on numerical simulations performed with modern aerodynamic and reactive flow solvers, this work underlines the interest of high-performance computing for solving flow in complex industrial configurations such as aircrafts, combustion chambers and turbomachines. Performance indicators related to parallel computing efficiency are presented, showing that establishing fair criterions is a difficult task for complex industrial applications. Examples of numerical simulations performed in industrial systems are also described with a particular interest for the computational time and the potential design improvements obtained with high-fidelity and multi-physics computing methods. These simulations use either unsteady Reynolds-averaged Navier-Stokes methods or large eddy simulation and deal with turbulent unsteady flows, such as coupled flow phenomena (thermo-acoustic instabilities, buffet, etc). Some examples of the difficulties with grid generation and data analysis are also presented when dealing with these complex industrial applications.

Complexity of Curved Glass Structures

Science.gov (United States)

Kosić, T.; Svetel, I.; Cekić, Z.

2017-11-01

Despite the increasing number of research on the architectural structures of curvilinear forms and technological and practical improvement of the glass production observed over recent years, there is still a lack of comprehensive codes and standards, recommendations and experience data linked to real-life curved glass structures applications regarding design, manufacture, use, performance and economy. However, more and more complex buildings and structures with the large areas of glass envelope geometrically complex shape are built every year. The aim of the presented research is to collect data on the existing design philosophy on curved glass structure cases. The investigation includes a survey about how architects and engineers deal with different design aspects of curved glass structures with a special focus on the design and construction process, glass types and structural and fixing systems. The current paper gives a brief overview of the survey findings.

Complexity-aware high efficiency video coding

CERN Document Server

Correa, Guilherme; Agostini, Luciano; Cruz, Luis A da Silva

2016-01-01

This book discusses computational complexity of High Efficiency Video Coding (HEVC) encoders with coverage extending from the analysis of HEVC compression efficiency and computational complexity to the reduction and scaling of its encoding complexity. After an introduction to the topic and a review of the state-of-the-art research in the field, the authors provide a detailed analysis of the HEVC encoding tools compression efficiency and computational complexity.  Readers will benefit from a set of algorithms for scaling the computational complexity of HEVC encoders, all of which take advantage from the flexibility of the frame partitioning structures allowed by the standard.  The authors also provide a set of early termination methods based on data mining and machine learning techniques, which are able to reduce the computational complexity required to find the best frame partitioning structures. The applicability of the proposed methods is finally exemplified with an encoding time control system that emplo...

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

Science.gov (United States)

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Computationally-optimized bone mechanical modeling from high-resolution structural images.

Directory of Open Access Journals (Sweden)

Jeremy F Magland

Full Text Available Image-based mechanical modeling of the complex micro-structure of human bone has shown promise as a non-invasive method for characterizing bone strength and fracture risk in vivo. In particular, elastic moduli obtained from image-derived micro-finite element (μFE simulations have been shown to correlate well with results obtained by mechanical testing of cadaveric bone. However, most existing large-scale finite-element simulation programs require significant computing resources, which hamper their use in common laboratory and clinical environments. In this work, we theoretically derive and computationally evaluate the resources needed to perform such simulations (in terms of computer memory and computation time, which are dependent on the number of finite elements in the image-derived bone model. A detailed description of our approach is provided, which is specifically optimized for μFE modeling of the complex three-dimensional architecture of trabecular bone. Our implementation includes domain decomposition for parallel computing, a novel stopping criterion, and a system for speeding up convergence by pre-iterating on coarser grids. The performance of the system is demonstrated on a dual quad-core Xeon 3.16 GHz CPUs equipped with 40 GB of RAM. Models of distal tibia derived from 3D in-vivo MR images in a patient comprising 200,000 elements required less than 30 seconds to converge (and 40 MB RAM. To illustrate the system's potential for large-scale μFE simulations, axial stiffness was estimated from high-resolution micro-CT images of a voxel array of 90 million elements comprising the human proximal femur in seven hours CPU time. In conclusion, the system described should enable image-based finite-element bone simulations in practical computation times on high-end desktop computers with applications to laboratory studies and clinical imaging.

Exponential rise of dynamical complexity in quantum computing through projections.

Science.gov (United States)

Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya

2014-10-10

The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.

Nitrosonium complexes of organic compounds. Structure and reactivity

International Nuclear Information System (INIS)

Borodkin, Gennady I; Shubin, Vyacheslav G

2001-01-01

Data on the structures and reactivities of nitrosonium complexes of organic compounds are systematised and generalised. The characteristic features of the electronic structure of the NO + cation are responsible for a wide structural variety of nitrosonium complexes. Reactions of nitrosonium complexes are described. The bibliography includes 172 references.

Computational design of RNAs with complex energy landscapes.

Science.gov (United States)

Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F

2013-12-01

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.

On the dimension of complex responses in nonlinear structural vibrations

Science.gov (United States)

Wiebe, R.; Spottswood, S. M.

2016-07-01

The ability to accurately model engineering systems under extreme dynamic loads would prove a major breakthrough in many aspects of aerospace, mechanical, and civil engineering. Extreme loads frequently induce both nonlinearities and coupling which increase the complexity of the response and the computational cost of finite element models. Dimension reduction has recently gained traction and promises the ability to distill dynamic responses down to a minimal dimension without sacrificing accuracy. In this context, the dimensionality of a response is related to the number of modes needed in a reduced order model to accurately simulate the response. Thus, an important step is characterizing the dimensionality of complex nonlinear responses of structures. In this work, the dimensionality of the nonlinear response of a post-buckled beam is investigated. Significant detail is dedicated to carefully introducing the experiment, the verification of a finite element model, and the dimensionality estimation algorithm as it is hoped that this system may help serve as a benchmark test case. It is shown that with minor modifications, the method of false nearest neighbors can quantitatively distinguish between the response dimension of various snap-through, non-snap-through, random, and deterministic loads. The state-space dimension of the nonlinear system in question increased from 2-to-10 as the system response moved from simple, low-level harmonic to chaotic snap-through. Beyond the problem studied herein, the techniques developed will serve as a prescriptive guide in developing fast and accurate dimensionally reduced models of nonlinear systems, and eventually as a tool for adaptive dimension-reduction in numerical modeling. The results are especially relevant in the aerospace industry for the design of thin structures such as beams, panels, and shells, which are all capable of spatio-temporally complex dynamic responses that are difficult and computationally expensive to

Computational complexity a quantitative perspective

CERN Document Server

Zimand, Marius

2004-01-01

There has been a common perception that computational complexity is a theory of "bad news" because its most typical results assert that various real-world and innocent-looking tasks are infeasible. In fact, "bad news" is a relative term, and, indeed, in some situations (e.g., in cryptography), we want an adversary to not be able to perform a certain task. However, a "bad news" result does not automatically become useful in such a scenario. For this to happen, its hardness features have to be quantitatively evaluated and shown to manifest extensively. The book undertakes a quantitative analysis of some of the major results in complexity that regard either classes of problems or individual concrete problems. The size of some important classes are studied using resource-bounded topological and measure-theoretical tools. In the case of individual problems, the book studies relevant quantitative attributes such as approximation properties or the number of hard inputs at each length. One chapter is dedicated to abs...

New computing systems, future computing environment, and their implications on structural analysis and design

Science.gov (United States)

Noor, Ahmed K.; Housner, Jerrold M.

1993-01-01

Recent advances in computer technology that are likely to impact structural analysis and design of flight vehicles are reviewed. A brief summary is given of the advances in microelectronics, networking technologies, and in the user-interface hardware and software. The major features of new and projected computing systems, including high performance computers, parallel processing machines, and small systems, are described. Advances in programming environments, numerical algorithms, and computational strategies for new computing systems are reviewed. The impact of the advances in computer technology on structural analysis and the design of flight vehicles is described. A scenario for future computing paradigms is presented, and the near-term needs in the computational structures area are outlined.

Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

Directory of Open Access Journals (Sweden)

Renata Ferrari

2016-02-01

Full Text Available Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g., ratio of surface to planar area underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km2. Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i branching coral colony (Acropora spp.; (ii reef area (400 m2; and (iii reef transect (2 km. At small scales, our method delivered models with <1 mm error over 90% of the surface area, while the accuracy at transect scale was 85.3% ± 6% (CI. Advantages are: no need for an a priori requirement for image size or resolution, no invasive techniques, cost-effectiveness, and utilization of existing imagery taken from off-the-shelf cameras (both monocular or stereo. This remote sensing method can be integrated to reef monitoring and improve our knowledge of key aspects of coral reef dynamics, from reef accretion to habitat provisioning and productivity, by measuring and up-scaling estimates of structural complexity.

Structure, function, and behaviour of computational models in systems biology.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens; Dittrich, Peter; Le Novère, Nicolas

2013-05-31

Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework - the meaning facets - which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model's components (structure), the meaning of the model's intended use (function), and the meaning of the model's dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.

Statistical screening of input variables in a complex computer code

International Nuclear Information System (INIS)

Krieger, T.J.

1982-01-01

A method is presented for ''statistical screening'' of input variables in a complex computer code. The object is to determine the ''effective'' or important input variables by estimating the relative magnitudes of their associated sensitivity coefficients. This is accomplished by performing a numerical experiment consisting of a relatively small number of computer runs with the code followed by a statistical analysis of the results. A formula for estimating the sensitivity coefficients is derived. Reference is made to an earlier work in which the method was applied to a complex reactor code with good results

Structure problems in the analog computation; Problemes de structure dans le calcul analogique

Energy Technology Data Exchange (ETDEWEB)

Braffort, P.L. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1957-07-01

The recent mathematical development showed the importance of elementary structures (algebraic, topological, etc.) in abeyance under the great domains of classical analysis. Such structures in analog computation are put in evidence and possible development of applied mathematics are discussed. It also studied the topological structures of the standard representation of analog schemes such as additional triangles, integrators, phase inverters and functions generators. The analog method gives only the function of the variable: time, as results of its computations. But the course of computation, for systems including reactive circuits, introduces order structures which are called 'chronological'. Finally, it showed that the approximation methods of ordinary numerical and digital computation present the same structure as these analog computation. The structure analysis permits fruitful comparisons between the several domains of applied mathematics and suggests new important domains of application for analog method. (M.P.)

Structure problems in the analog computation; Problemes de structure dans le calcul analogique

Energy Technology Data Exchange (ETDEWEB)

Braffort, P L [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1957-07-01

The recent mathematical development showed the importance of elementary structures (algebraic, topological, etc.) in abeyance under the great domains of classical analysis. Such structures in analog computation are put in evidence and possible development of applied mathematics are discussed. It also studied the topological structures of the standard representation of analog schemes such as additional triangles, integrators, phase inverters and functions generators. The analog method gives only the function of the variable: time, as results of its computations. But the course of computation, for systems including reactive circuits, introduces order structures which are called 'chronological'. Finally, it showed that the approximation methods of ordinary numerical and digital computation present the same structure as these analog computation. The structure analysis permits fruitful comparisons between the several domains of applied mathematics and suggests new important domains of application for analog method. (M.P.)

Multiresolution Computation of Conformal Structures of Surfaces

Directory of Open Access Journals (Sweden)

Xianfeng Gu

2003-10-01

Full Text Available An efficient multiresolution method to compute global conformal structures of nonzero genus triangle meshes is introduced. The homology, cohomology groups of meshes are computed explicitly, then a basis of harmonic one forms and a basis of holomorphic one forms are constructed. A progressive mesh is generated to represent the original surface at different resolutions. The conformal structure is computed for the coarse level first, then used as the estimation for that of the finer level, by using conjugate gradient method it can be refined to the conformal structure of the finer level.

Charge transfer complex between 2,3-diaminopyridine with chloranilic acid. Synthesis, characterization and DFT, TD-DFT computational studies

Science.gov (United States)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2018-05-01

New charge transfer complex (CTC) between the electron donor 2,3-diaminopyridine (DAP) with the electron acceptor chloranilic (CLA) acid has been synthesized and characterized experimentally and theoretically using a variety of physicochemical techniques. The experimental work included the use of elemental analysis, UV-vis, IR and 1H NMR studies to characterize the complex. Electronic spectra have been carried out in different hydrogen bonded solvents, methanol (MeOH), acetonitrile (AN) and 1:1 mixture from AN-MeOH. The molecular composition of the complex was identified to be 1:1 from Jobs and molar ratio methods. The stability constant was determined using minimum-maximum absorbances method where it recorded high values confirming the high stability of the formed complex. The solid complex was prepared and characterized by elemental analysis that confirmed its formation in 1:1 stoichiometric ratio. Both IR and NMR studies asserted the existence of proton and charge transfers in the formed complex. For supporting the experimental results, DFT computations were carried out using B3LYP/6-31G(d,p) method to compute the optimized structures of the reactants and complex, their geometrical parameters, reactivity parameters, molecular electrostatic potential map and frontier molecular orbitals. The analysis of DFT results strongly confirmed the high stability of the formed complex based on existing charge transfer beside proton transfer hydrogen bonding concordant with experimental results. The origin of electronic spectra was analyzed using TD-DFT method where the observed λmax are strongly consisted with the computed ones. TD-DFT showed the contributed states for various electronic transitions.

In silico Interrogation of Insect Central Complex Suggests Computational Roles for the Ellipsoid Body in Spatial Navigation

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Vincenzo G. Fiore

2017-08-01

Full Text Available The central complex in the insect brain is a composite of midline neuropils involved in processing sensory cues and mediating behavioral outputs to orchestrate spatial navigation. Despite recent advances, however, the neural mechanisms underlying sensory integration and motor action selections have remained largely elusive. In particular, it is not yet understood how the central complex exploits sensory inputs to realize motor functions associated with spatial navigation. Here we report an in silico interrogation of central complex-mediated spatial navigation with a special emphasis on the ellipsoid body. Based on known connectivity and function, we developed a computational model to test how the local connectome of the central complex can mediate sensorimotor integration to guide different forms of behavioral outputs. Our simulations show integration of multiple sensory sources can be effectively performed in the ellipsoid body. This processed information is used to trigger continuous sequences of action selections resulting in self-motion, obstacle avoidance and the navigation of simulated environments of varying complexity. The motor responses to perceived sensory stimuli can be stored in the neural structure of the central complex to simulate navigation relying on a collective of guidance cues, akin to sensory-driven innate or habitual behaviors. By comparing behaviors under different conditions of accessible sources of input information, we show the simulated insect computes visual inputs and body posture to estimate its position in space. Finally, we tested whether the local connectome of the central complex might also allow the flexibility required to recall an intentional behavioral sequence, among different courses of actions. Our simulations suggest that the central complex can encode combined representations of motor and spatial information to pursue a goal and thus successfully guide orientation behavior. Together, the observed

In silico Interrogation of Insect Central Complex Suggests Computational Roles for the Ellipsoid Body in Spatial Navigation.

Science.gov (United States)

Fiore, Vincenzo G; Kottler, Benjamin; Gu, Xiaosi; Hirth, Frank

2017-01-01

The central complex in the insect brain is a composite of midline neuropils involved in processing sensory cues and mediating behavioral outputs to orchestrate spatial navigation. Despite recent advances, however, the neural mechanisms underlying sensory integration and motor action selections have remained largely elusive. In particular, it is not yet understood how the central complex exploits sensory inputs to realize motor functions associated with spatial navigation. Here we report an in silico interrogation of central complex-mediated spatial navigation with a special emphasis on the ellipsoid body. Based on known connectivity and function, we developed a computational model to test how the local connectome of the central complex can mediate sensorimotor integration to guide different forms of behavioral outputs. Our simulations show integration of multiple sensory sources can be effectively performed in the ellipsoid body. This processed information is used to trigger continuous sequences of action selections resulting in self-motion, obstacle avoidance and the navigation of simulated environments of varying complexity. The motor responses to perceived sensory stimuli can be stored in the neural structure of the central complex to simulate navigation relying on a collective of guidance cues, akin to sensory-driven innate or habitual behaviors. By comparing behaviors under different conditions of accessible sources of input information, we show the simulated insect computes visual inputs and body posture to estimate its position in space. Finally, we tested whether the local connectome of the central complex might also allow the flexibility required to recall an intentional behavioral sequence, among different courses of actions. Our simulations suggest that the central complex can encode combined representations of motor and spatial information to pursue a goal and thus successfully guide orientation behavior. Together, the observed computational features

Synthesis and structure of cerium nitrosocarbonylcyanmethanid complex

International Nuclear Information System (INIS)

Gerasimenko, H.; Scopenko, V.V.; Kapshuk, A.A.

1998-01-01

Full text: The complex compound [CeL 4 Dy 2 ]Na*2Ac (where L- nitrosocarbonylcyanmethanid, Dy -- dipyridile, Ac - acetone) were synthesised by interaction of cerium chloride and sodium nitrosocarbonylcyanmethanid from acetone solution. After two hours of mixing the dipyridil solution in acetone was added for complex stabilization. After filtration solution was put to desiccator for crystallisation. The complex was studied using IR- and UV-spectroscopy. The structure of the complex was determined using X-ray structure analysis. It was found that the structure of the complex belongs to orthorhombic Pna2(1) syngony with the unit cell parameters 17.010, 16.280 and 16.340Angstroms, respectively. It was found that cerium in the compound was eight co-ordinated. Four nitroso ligands were co-ordinated by bidentate bridge method and two dipyridiles by bidentate-cycle method

Development of Onboard Computer Complex for Russian Segment of ISS

Science.gov (United States)

Branets, V.; Brand, G.; Vlasov, R.; Graf, I.; Clubb, J.; Mikrin, E.; Samitov, R.

1998-01-01

Report present a description of the Onboard Computer Complex (CC) that was developed during the period of 1994-1998 for the Russian Segment of ISS. The system was developed in co-operation with NASA and ESA. ESA developed a new computation system under the RSC Energia Technical Assignment, called DMS-R. The CC also includes elements developed by Russian experts and organizations. A general architecture of the computer system and the characteristics of primary elements of this system are described. The system was integrated at RSC Energia with the participation of American and European specialists. The report contains information on software simulators, verification and de-bugging facilities witch were been developed for both stand-alone and integrated tests and verification. This CC serves as the basis for the Russian Segment Onboard Control Complex on ISS.

Computing optimal interfacial structure of modulated phases

OpenAIRE

Xu, Jie; Wang, Chu; Shi, An-Chang; Zhang, Pingwen

2016-01-01

We propose a general framework of computing interfacial structures between two modulated phases. Specifically we propose to use a computational box consisting of two half spaces, each occupied by a modulated phase with given position and orientation. The boundary conditions and basis functions are chosen to be commensurate with the bulk structures. It is observed that the ordered nature of modulated structures stabilizes the interface, which enables us to obtain optimal interfacial structures...

Improved computation method in residual life estimation of structural components

Directory of Open Access Journals (Sweden)

Maksimović Stevan M.

2013-01-01

Full Text Available This work considers the numerical computation methods and procedures for the fatigue crack growth predicting of cracked notched structural components. Computation method is based on fatigue life prediction using the strain energy density approach. Based on the strain energy density (SED theory, a fatigue crack growth model is developed to predict the lifetime of fatigue crack growth for single or mixed mode cracks. The model is based on an equation expressed in terms of low cycle fatigue parameters. Attention is focused on crack growth analysis of structural components under variable amplitude loads. Crack growth is largely influenced by the effect of the plastic zone at the front of the crack. To obtain efficient computation model plasticity-induced crack closure phenomenon is considered during fatigue crack growth. The use of the strain energy density method is efficient for fatigue crack growth prediction under cyclic loading in damaged structural components. Strain energy density method is easy for engineering applications since it does not require any additional determination of fatigue parameters (those would need to be separately determined for fatigue crack propagation phase, and low cyclic fatigue parameters are used instead. Accurate determination of fatigue crack closure has been a complex task for years. The influence of this phenomenon can be considered by means of experimental and numerical methods. Both of these models are considered. Finite element analysis (FEA has been shown to be a powerful and useful tool1,6 to analyze crack growth and crack closure effects. Computation results are compared with available experimental results. [Projekat Ministarstva nauke Republike Srbije, br. OI 174001

Some Comparisons of Complexity in Dictionary-Based and Linear Computational Models

Czech Academy of Sciences Publication Activity Database

Gnecco, G.; Kůrková, Věra; Sanguineti, M.

2011-01-01

Roč. 24, č. 2 (2011), s. 171-182 ISSN 0893-6080 R&D Project s: GA ČR GA201/08/1744 Grant - others:CNR - AV ČR project 2010-2012(XE) Complexity of Neural-Network and Kernel Computational Models Institutional research plan: CEZ:AV0Z10300504 Keywords : linear approximation schemes * variable-basis approximation schemes * model complexity * worst-case errors * neural networks * kernel models Subject RIV: IN - Informatics, Computer Science Impact factor: 2.182, year: 2011

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

Science.gov (United States)

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure.

Science.gov (United States)

Peng, Wei; Wang, Jianxin; Zhao, Bihai; Wang, Lusheng

2015-01-01

Protein complexes play a significant role in understanding the underlying mechanism of most cellular functions. Recently, many researchers have explored computational methods to identify protein complexes from protein-protein interaction (PPI) networks. One group of researchers focus on detecting local dense subgraphs which correspond to protein complexes by considering local neighbors. The drawback of this kind of approach is that the global information of the networks is ignored. Some methods such as Markov Clustering algorithm (MCL), PageRank-Nibble are proposed to find protein complexes based on random walk technique which can exploit the global structure of networks. However, these methods ignore the inherent core-attachment structure of protein complexes and treat adjacent node equally. In this paper, we design a weighted PageRank-Nibble algorithm which assigns each adjacent node with different probability, and propose a novel method named WPNCA to detect protein complex from PPI networks by using weighted PageRank-Nibble algorithm and core-attachment structure. Firstly, WPNCA partitions the PPI networks into multiple dense clusters by using weighted PageRank-Nibble algorithm. Then the cores of these clusters are detected and the rest of proteins in the clusters will be selected as attachments to form the final predicted protein complexes. The experiments on yeast data show that WPNCA outperforms the existing methods in terms of both accuracy and p-value. The software for WPNCA is available at "http://netlab.csu.edu.cn/bioinfomatics/weipeng/WPNCA/download.html".

Supramolecular structure of glibenclamide and β-cyclodextrins complexes.

Science.gov (United States)

Lucio, David; Irache, Juan Manuel; Font, María; Martínez-Ohárriz, María Cristina

2017-09-15

Glibenclamide is an antidiabetic drug showing low bioavailability as consequence of its low solubility. To solve this drawback, the interaction with cyclodextrins has been proposed. The formation of GB-βCDs inclusion complexes was carried out using different methods, βCD derivatives and drug-to-cyclodextrin ratios. The structures of the corresponding complexes have been studied by molecular modelling, X-ray diffraction and differential thermal analysis. The dissolution behavior of inclusion complexes has been compared to that of pure GB. Dimeric inclusion complexes were obtained with different CD disposals, head-to-head for βCD and head-to-tail for HPβCD and RMβCD. Amorphous inclusion complexes were obtained by employing methods of freeze-drying or coevaporation in ammonia-water. However, crystalline structures were formed by kneading and coevaporation in ethanol/water in the case of GB-βCD complexes. The arrangement of these structures depended on the GB:βCD ratio, yielding cage type structures for 1:3 and 1:5 ratios and channel-type structures for higher GB contents. The amount of GB released and its dissolution rate was considerably increased by the use of amorphous inclusion complexes; whereas, slower GB release rates were found from crystalline inclusion complexes formed by kneading or coevaporation in ethanol/water. In addition, it was found that the porous structure strongly conditioned the GB dissolution rate from crystalline products. Copyright © 2017 Elsevier B.V. All rights reserved.

Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5

Science.gov (United States)

Tamamis, Phanourios; Floudas, Christodoulos A.

2014-06-01

CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.

Algorithms and file structures for computational geometry

International Nuclear Information System (INIS)

Hinrichs, K.; Nievergelt, J.

1983-01-01

Algorithms for solving geometric problems and file structures for storing large amounts of geometric data are of increasing importance in computer graphics and computer-aided design. As examples of recent progress in computational geometry, we explain plane-sweep algorithms, which solve various topological and geometric problems efficiently; and we present the grid file, an adaptable, symmetric multi-key file structure that provides efficient access to multi-dimensional data along any space dimension. (orig.)

Modern structure of marketing communications complex

Directory of Open Access Journals (Sweden)

Hrebenyukova Elena

2015-08-01

Full Text Available The article presents the results of the desk research, in which the current structure of the marketing communications complex was analyzed. According to the results of the content analysis of scientific and educational literature in marketing it was proved that there is a certain structural asymmetry in today's complex of marketing communication: the rejection of impersonal tools and actualization of those which make possible personalized communication with the consumer.

Low Computational Complexity Network Coding For Mobile Networks

DEFF Research Database (Denmark)

Heide, Janus

2012-01-01

Network Coding (NC) is a technique that can provide benefits in many types of networks, some examples from wireless networks are: In relay networks, either the physical or the data link layer, to reduce the number of transmissions. In reliable multicast, to reduce the amount of signaling and enable......-flow coding technique. One of the key challenges of this technique is its inherent computational complexity which can lead to high computational load and energy consumption in particular on the mobile platforms that are the target platform in this work. To increase the coding throughput several...

Comparing Virtual and Physical Robotics Environments for Supporting Complex Systems and Computational Thinking

Science.gov (United States)

Berland, Matthew; Wilensky, Uri

2015-01-01

Both complex systems methods (such as agent-based modeling) and computational methods (such as programming) provide powerful ways for students to understand new phenomena. To understand how to effectively teach complex systems and computational content to younger students, we conducted a study in four urban middle school classrooms comparing…

Complex structures in the Nash-Moser category

DEFF Research Database (Denmark)

Gravesen, Jens

1989-01-01

Working in the Nash-Moser category, it is shown that the harmonic and holomorphic differentials and the Weierstrass points on a closed Riemann surface depend smoothly on the complex structure. It is also shown that the space of complex structures on any compact surface forms a principal bundle over...

The complexity of computing the MCD-estimator

DEFF Research Database (Denmark)

Bernholt, T.; Fischer, Paul

2004-01-01

In modem statistics the robust estimation of parameters is a central problem, i.e., an estimation that is not or only slightly affected by outliers in the data. The minimum covariance determinant (MCD) estimator (J. Amer. Statist. Assoc. 79 (1984) 871) is probably one of the most important robust...... estimators of location and scatter. The complexity of computing the MCD, however, was unknown and generally thought to be exponential even if the dimensionality of the data is fixed. Here we present a polynomial time algorithm for MCD for fixed dimension of the data. In contrast we show that computing...... the MCD-estimator is NP-hard if the dimension varies. (C) 2004 Elsevier B.V. All rights reserved....

Complex photonic structures

International Nuclear Information System (INIS)

Wiersma, D.S.

2013-01-01

We discuss in detail the optical properties of complex photonic structures, in particular those with a dominating disorder component. We will focus on their general transport properties, as well as on their use as light sources (random lasers). The basis for the theory of multiple light scattering in random systems will be explained as a tutorial introduction to the topic, including the explicit calculation of the effect of coherent backscattering. We will discuss various structures that go beyond regular disordered ones, in particular Levy glasses, liquid crystals, and quasicrystals, and show examples of their optical properties both from a conceptual and practical point of view.

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

Science.gov (United States)

Hadjidoukas, P. E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

2015-03-01

We present Π4U, an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

International Nuclear Information System (INIS)

Hadjidoukas, P.E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

2015-01-01

We present Π4U, 1 an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow

Complex cellular logic computation using ribocomputing devices.

Science.gov (United States)

Green, Alexander A; Kim, Jongmin; Ma, Duo; Silver, Pamela A; Collins, James J; Yin, Peng

2017-08-03

Synthetic biology aims to develop engineering-driven approaches to the programming of cellular functions that could yield transformative technologies. Synthetic gene circuits that combine DNA, protein, and RNA components have demonstrated a range of functions such as bistability, oscillation, feedback, and logic capabilities. However, it remains challenging to scale up these circuits owing to the limited number of designable, orthogonal, high-performance parts, the empirical and often tedious composition rules, and the requirements for substantial resources for encoding and operation. Here, we report a strategy for constructing RNA-only nanodevices to evaluate complex logic in living cells. Our 'ribocomputing' systems are composed of de-novo-designed parts and operate through predictable and designable base-pairing rules, allowing the effective in silico design of computing devices with prescribed configurations and functions in complex cellular environments. These devices operate at the post-transcriptional level and use an extended RNA transcript to co-localize all circuit sensing, computation, signal transduction, and output elements in the same self-assembled molecular complex, which reduces diffusion-mediated signal losses, lowers metabolic cost, and improves circuit reliability. We demonstrate that ribocomputing devices in Escherichia coli can evaluate two-input logic with a dynamic range up to 900-fold and scale them to four-input AND, six-input OR, and a complex 12-input expression (A1 AND A2 AND NOT A1*) OR (B1 AND B2 AND NOT B2*) OR (C1 AND C2) OR (D1 AND D2) OR (E1 AND E2). Successful operation of ribocomputing devices based on programmable RNA interactions suggests that systems employing the same design principles could be implemented in other host organisms or in extracellular settings.

Structural and Topology Optimization of Complex Civil Engineering Structures

DEFF Research Database (Denmark)

Hald, Frederik; Kirkegaard, Poul Henning; Andersen, Lars Vabbersgaard

2013-01-01

This paper shows the use of topology optimization for finding an optimized form for civil engineering structures. Today topology optimization and shape optimization have been integrated in several commercial finite element codes. Here, the topology of two complex civil engineering structures...

Complex data modeling and computationally intensive methods for estimation and prediction

CERN Document Server

Secchi, Piercesare; Advances in Complex Data Modeling and Computational Methods in Statistics

2015-01-01

The book is addressed to statisticians working at the forefront of the statistical analysis of complex and high dimensional data and offers a wide variety of statistical models, computer intensive methods and applications: network inference from the analysis of high dimensional data; new developments for bootstrapping complex data; regression analysis for measuring the downsize reputational risk; statistical methods for research on the human genome dynamics; inference in non-euclidean settings and for shape data; Bayesian methods for reliability and the analysis of complex data; methodological issues in using administrative data for clinical and epidemiological research; regression models with differential regularization; geostatistical methods for mobility analysis through mobile phone data exploration. This volume is the result of a careful selection among the contributions presented at the conference "S.Co.2013: Complex data modeling and computationally intensive methods for estimation and prediction" held...

Theoretical Studies on the Electronic Structures and Properties of Complex Ceramic Crystals and Novel Materials

Energy Technology Data Exchange (ETDEWEB)

Ching, Wai-Yim

2012-01-14

This project is a continuation of a long program supported by the Office of Basic Energy Science in the Office of Science of DOE for many years. The final three-year continuation started on November 1, 2005 with additional 1 year extension to October 30, 2009. The project was then granted a two-year No Cost Extension which officially ended on October 30, 2011. This report covers the activities within this six year period with emphasis on the work completed within the last 3 years. A total of 44 papers with acknowledgement to this grant were published or submitted. The overall objectives of this project are as follows. These objectives have been evolved over the six year period: (1) To use the state-of-the-art computational methods to investigate the electronic structures of complex ceramics and other novel crystals. (2) To further investigate the defects, surfaces/interfaces and microstructures in complex materials using large scale modeling. (3) To extend the study on ceramic materials to more complex bioceramic crystals. (4) To initiate the study on soft condensed matters including water and biomolecules. (5) To focus on the spectroscopic studies of different materials especially on the ELNES and XANES spectral calculations and their applications related to experimental techniques. (6) To develop and refine computational methods to be effectively executed on DOE supercomputers. (7) To evaluate mechanical properties of different crystals and those containing defects and relate them to the fundamental electronic structures. (8) To promote and publicize the first-principles OLCAO method developed by the PI (under DOE support for many years) for applications to large complex material systems. (9) To train a new generation of graduate students and postdoctoral fellows in modern computational materials science and condensed matter physics. (10) To establish effective international and domestic collaborations with both experimentalists and theorists in materials

Complex layered materials and periodic electromagnetic band-gap structures: Concepts, characterizations, and applications

Science.gov (United States)

Mosallaei, Hossein

The main objective of this dissertation is to characterize and create insight into the electromagnetic performances of two classes of composite structures, namely, complex multi-layered media and periodic Electromagnetic Band-Gap (EBG) structures. The advanced and diversified computational techniques are applied to obtain their unique propagation characteristics and integrate the results into some novel applications. In the first part of this dissertation, the vector wave solution of Maxwell's equations is integrated with the Genetic Algorithm (GA) optimization method to provide a powerful technique for characterizing multi-layered materials, and obtaining their optimal designs. The developed method is successfully applied to determine the optimal composite coatings for Radar Cross Section (RCS) reduction of canonical structures. Both monostatic and bistatic scatterings are explored. A GA with hybrid planar/curved surface implementation is also introduced to efficiently obtain the optimal absorbing materials for curved structures. Furthermore, design optimization of the non-uniform Luneburg and 2-shell spherical lens antennas utilizing modal solution/GA-adaptive-cost function is presented. The lens antennas are effectively optimized for both high gain and suppressed grating lobes. The second part demonstrates the development of an advanced computational engine, which accurately computes the broadband characteristics of challenging periodic electromagnetic band-gap structures. This method utilizes the Finite Difference Time Domain (FDTD) technique with Periodic Boundary Condition/Perfectly Matched Layer (PBC/PML), which is efficiently integrated with the Prony scheme. The computational technique is successfully applied to characterize and present the unique propagation performances of different classes of periodic structures such as Frequency Selective Surfaces (FSS), Photonic Band-Gap (PBG) materials, and Left-Handed (LH) composite media. The results are

Methodology for Simulation and Analysis of Complex Adaptive Supply Network Structure and Dynamics Using Information Theory

Directory of Open Access Journals (Sweden)

Joshua Rodewald

2016-10-01

Full Text Available Supply networks existing today in many industries can behave as complex adaptive systems making them more difficult to analyze and assess. Being able to fully understand both the complex static and dynamic structures of a complex adaptive supply network (CASN are key to being able to make more informed management decisions and prioritize resources and production throughout the network. Previous efforts to model and analyze CASN have been impeded by the complex, dynamic nature of the systems. However, drawing from other complex adaptive systems sciences, information theory provides a model-free methodology removing many of those barriers, especially concerning complex network structure and dynamics. With minimal information about the network nodes, transfer entropy can be used to reverse engineer the network structure while local transfer entropy can be used to analyze the network structure’s dynamics. Both simulated and real-world networks were analyzed using this methodology. Applying the methodology to CASNs allows the practitioner to capitalize on observations from the highly multidisciplinary field of information theory which provides insights into CASN’s self-organization, emergence, stability/instability, and distributed computation. This not only provides managers with a more thorough understanding of a system’s structure and dynamics for management purposes, but also opens up research opportunities into eventual strategies to monitor and manage emergence and adaption within the environment.

Flow simulations about steady-complex and unsteady moving configurations using structured-overlapped and unstructured grids

Science.gov (United States)

Newman, James C., III

1995-01-01

The limiting factor in simulating flows past realistic configurations of interest has been the discretization of the physical domain on which the governing equations of fluid flow may be solved. In an attempt to circumvent this problem, many Computational Fluid Dynamic (CFD) methodologies that are based on different grid generation and domain decomposition techniques have been developed. However, due to the costs involved and expertise required, very few comparative studies between these methods have been performed. In the present work, the two CFD methodologies which show the most promise for treating complex three-dimensional configurations as well as unsteady moving boundary problems are evaluated. These are namely the structured-overlapped and the unstructured grid schemes. Both methods use a cell centered, finite volume, upwind approach. The structured-overlapped algorithm uses an approximately factored, alternating direction implicit scheme to perform the time integration, whereas, the unstructured algorithm uses an explicit Runge-Kutta method. To examine the accuracy, efficiency, and limitations of each scheme, they are applied to the same steady complex multicomponent configurations and unsteady moving boundary problems. The steady complex cases consist of computing the subsonic flow about a two-dimensional high-lift multielement airfoil and the transonic flow about a three-dimensional wing/pylon/finned store assembly. The unsteady moving boundary problems are a forced pitching oscillation of an airfoil in a transonic freestream and a two-dimensional, subsonic airfoil/store separation sequence. Accuracy was accessed through the comparison of computed and experimentally measured pressure coefficient data on several of the wing/pylon/finned store assembly's components and at numerous angles-of-attack for the pitching airfoil. From this study, it was found that both the structured-overlapped and the unstructured grid schemes yielded flow solutions of

Study of complex modes

International Nuclear Information System (INIS)

Pastrnak, J.W.

1986-01-01

This eighteen-month study has been successful in providing the designer and analyst with qualitative guidelines on the occurrence of complex modes in the dynamics of linear structures, and also in developing computer codes for determining quantitatively which vibration modes are complex and to what degree. The presence of complex modes in a test structure has been verified. Finite element analysis of a structure with non-proportional dumping has been performed. A partial differential equation has been formed to eliminate possible modeling errors

Computational predictions of zinc oxide hollow structures

Science.gov (United States)

Tuoc, Vu Ngoc; Huan, Tran Doan; Thao, Nguyen Thi

2018-03-01

Nanoporous materials are emerging as potential candidates for a wide range of technological applications in environment, electronic, and optoelectronics, to name just a few. Within this active research area, experimental works are predominant while theoretical/computational prediction and study of these materials face some intrinsic challenges, one of them is how to predict porous structures. We propose a computationally and technically feasible approach for predicting zinc oxide structures with hollows at the nano scale. The designed zinc oxide hollow structures are studied with computations using the density functional tight binding and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications.

STARS: An Integrated, Multidisciplinary, Finite-Element, Structural, Fluids, Aeroelastic, and Aeroservoelastic Analysis Computer Program

Science.gov (United States)

Gupta, K. K.

1997-01-01

A multidisciplinary, finite element-based, highly graphics-oriented, linear and nonlinear analysis capability that includes such disciplines as structures, heat transfer, linear aerodynamics, computational fluid dynamics, and controls engineering has been achieved by integrating several new modules in the original STARS (STructural Analysis RoutineS) computer program. Each individual analysis module is general-purpose in nature and is effectively integrated to yield aeroelastic and aeroservoelastic solutions of complex engineering problems. Examples of advanced NASA Dryden Flight Research Center projects analyzed by the code in recent years include the X-29A, F-18 High Alpha Research Vehicle/Thrust Vectoring Control System, B-52/Pegasus Generic Hypersonics, National AeroSpace Plane (NASP), SR-71/Hypersonic Launch Vehicle, and High Speed Civil Transport (HSCT) projects. Extensive graphics capabilities exist for convenient model development and postprocessing of analysis results. The program is written in modular form in standard FORTRAN language to run on a variety of computers, such as the IBM RISC/6000, SGI, DEC, Cray, and personal computer; associated graphics codes use OpenGL and IBM/graPHIGS language for color depiction. This program is available from COSMIC, the NASA agency for distribution of computer programs.

Complex systems relationships between control, communications and computing

CERN Document Server

2016-01-01

This book gives a wide-ranging description of the many facets of complex dynamic networks and systems within an infrastructure provided by integrated control and supervision: envisioning, design, experimental exploration, and implementation. The theoretical contributions and the case studies presented can reach control goals beyond those of stabilization and output regulation or even of adaptive control. Reporting on work of the Control of Complex Systems (COSY) research program, Complex Systems follows from and expands upon an earlier collection: Control of Complex Systems by introducing novel theoretical techniques for hard-to-control networks and systems. The major common feature of all the superficially diverse contributions encompassed by this book is that of spotting and exploiting possible areas of mutual reinforcement between control, computing and communications. These help readers to achieve not only robust stable plant system operation but also properties such as collective adaptivity, integrity an...

Computational studies of a paramagnetic planar dibenzotetraaza[14]annulene Ni(II) complex.

Science.gov (United States)

Rabaâ, Hassan; Khaledi, Hamid; Olmstead, Marilyn M; Sundholm, Dage

2015-05-28

A square-planar Ni(II) dibenzotetraaza[14]annulene complex substituted with two 3,3-dimethylindolenine groups in the meso positions has recently been synthesized and characterized experimentally. In the solid-state, the Ni(II) complex forms linear π-interacting stacks with Ni···Ni separations of 3.448(2) Å. Measurements of the temperature dependence of the magnetic susceptibility revealed a drastic change in the magnetic properties at a temperature of 13 K, indicating a transition from low-to-high spin states. The molecular structures of the free-base ligand, the lowest singlet, and triplet states of the monomer and the dimer of the Ni complex have been studied computationally using density functional theory (DFT) and ab initio correlation levels of theory. In calculations at the second-order Møller-Plesset (MP2) perturbation theory level, a large energy of 260 kcal mol(-1) was obtained for the singlet-triplet splitting, suggesting that an alternative explanation of the observed magnetic properties is needed. The large energy splitting between the singlet and triplet states suggests that the observed change in the magnetism at very low temperatures is due to spin-orbit coupling effects originating from weak interactions between the fine-structure states of the Ni cations in the complex. The lowest electronic excitation energies of the dibenzotetraaza[14]annulene Ni(II) complex calculated at the time-dependent density functional theory (TDDFT) levels are in good agreement with values deduced from the experimental UV-vis spectrum. Calculations at the second-order algebraic-diagrammatic construction (ADC(2)) level on the dimer of the meso-substituted 3,3-dimethylindolenine dibenzotetraaza[14] annulene Ni(II) complex yielded Stokes shifts of 85-100 nm for the lowest excited singlet states. Calculations of the strength of the magnetically induced ring current for the free-base 3,3-dimethylindolenine-substituted dibenzotetraaza[14]annulene show that the annulene

Complexity estimates based on integral transforms induced by computational units

Czech Academy of Sciences Publication Activity Database

Kůrková, Věra

2012-01-01

Roč. 33, September (2012), s. 160-167 ISSN 0893-6080 R&D Projects: GA ČR GAP202/11/1368 Institutional research plan: CEZ:AV0Z10300504 Institutional support: RVO:67985807 Keywords : neural networks * estimates of model complexity * approximation from a dictionary * integral transforms * norms induced by computational units Subject RIV: IN - Informatics, Computer Science Impact factor: 1.927, year: 2012

An approach to first principles electronic structure calculation by symbolic-numeric computation

Directory of Open Access Journals (Sweden)

Akihito Kikuchi

2013-04-01

Full Text Available There is a wide variety of electronic structure calculation cooperating with symbolic computation. The main purpose of the latter is to play an auxiliary role (but not without importance to the former. In the field of quantum physics [1-9], researchers sometimes have to handle complicated mathematical expressions, whose derivation seems almost beyond human power. Thus one resorts to the intensive use of computers, namely, symbolic computation [10-16]. Examples of this can be seen in various topics: atomic energy levels, molecular dynamics, molecular energy and spectra, collision and scattering, lattice spin models and so on [16]. How to obtain molecular integrals analytically or how to manipulate complex formulas in many body interactions, is one such problem. In the former, when one uses special atomic basis for a specific purpose, to express the integrals by the combination of already known analytic functions, may sometimes be very difficult. In the latter, one must rearrange a number of creation and annihilation operators in a suitable order and calculate the analytical expectation value. It is usual that a quantitative and massive computation follows a symbolic one; for the convenience of the numerical computation, it is necessary to reduce a complicated analytic expression into a tractable and computable form. This is the main motive for the introduction of the symbolic computation as a forerunner of the numerical one and their collaboration has won considerable successes. The present work should be classified as one such trial. Meanwhile, the use of symbolic computation in the present work is not limited to indirect and auxiliary part to the numerical computation. The present work can be applicable to a direct and quantitative estimation of the electronic structure, skipping conventional computational methods.

Basic design of parallel computational program for probabilistic structural analysis

International Nuclear Information System (INIS)

Kaji, Yoshiyuki; Arai, Taketoshi; Gu, Wenwei; Nakamura, Hitoshi

1999-06-01

In our laboratory, for 'development of damage evaluation method of structural brittle materials by microscopic fracture mechanics and probabilistic theory' (nuclear computational science cross-over research) we examine computational method related to super parallel computation system which is coupled with material strength theory based on microscopic fracture mechanics for latent cracks and continuum structural model to develop new structural reliability evaluation methods for ceramic structures. This technical report is the review results regarding probabilistic structural mechanics theory, basic terms of formula and program methods of parallel computation which are related to principal terms in basic design of computational mechanics program. (author)

Basic design of parallel computational program for probabilistic structural analysis

Energy Technology Data Exchange (ETDEWEB)

Kaji, Yoshiyuki; Arai, Taketoshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Gu, Wenwei; Nakamura, Hitoshi

1999-06-01

In our laboratory, for `development of damage evaluation method of structural brittle materials by microscopic fracture mechanics and probabilistic theory` (nuclear computational science cross-over research) we examine computational method related to super parallel computation system which is coupled with material strength theory based on microscopic fracture mechanics for latent cracks and continuum structural model to develop new structural reliability evaluation methods for ceramic structures. This technical report is the review results regarding probabilistic structural mechanics theory, basic terms of formula and program methods of parallel computation which are related to principal terms in basic design of computational mechanics program. (author)

Recent advances in computational structural reliability analysis methods

Science.gov (United States)

Thacker, Ben H.; Wu, Y.-T.; Millwater, Harry R.; Torng, Tony Y.; Riha, David S.

1993-10-01

The goal of structural reliability analysis is to determine the probability that the structure will adequately perform its intended function when operating under the given environmental conditions. Thus, the notion of reliability admits the possibility of failure. Given the fact that many different modes of failure are usually possible, achievement of this goal is a formidable task, especially for large, complex structural systems. The traditional (deterministic) design methodology attempts to assure reliability by the application of safety factors and conservative assumptions. However, the safety factor approach lacks a quantitative basis in that the level of reliability is never known and usually results in overly conservative designs because of compounding conservatisms. Furthermore, problem parameters that control the reliability are not identified, nor their importance evaluated. A summary of recent advances in computational structural reliability assessment is presented. A significant level of activity in the research and development community was seen recently, much of which was directed towards the prediction of failure probabilities for single mode failures. The focus is to present some early results and demonstrations of advanced reliability methods applied to structural system problems. This includes structures that can fail as a result of multiple component failures (e.g., a redundant truss), or structural components that may fail due to multiple interacting failure modes (e.g., excessive deflection, resonate vibration, or creep rupture). From these results, some observations and recommendations are made with regard to future research needs.

Current topics in pure and computational complex analysis

CERN Document Server

Dorff, Michael; Lahiri, Indrajit

2014-01-01

The book contains 13 articles, some of which are survey articles and others research papers. Written by eminent mathematicians, these articles were presented at the International Workshop on Complex Analysis and Its Applications held at Walchand College of Engineering, Sangli. All the contributing authors are actively engaged in research fields related to the topic of the book. The workshop offered a comprehensive exposition of the recent developments in geometric functions theory, planar harmonic mappings, entire and meromorphic functions and their applications, both theoretical and computational. The recent developments in complex analysis and its applications play a crucial role in research in many disciplines.

A method for the calculation of collision strengths for complex atomic structures based on Slater parameter optimisation

International Nuclear Information System (INIS)

Fawcett, B.C.; Mason, H.E.

1989-02-01

This report presents details of a new method to enable the computation of collision strengths for complex ions which is adapted from long established optimisation techniques previously applied to the calculation of atomic structures and oscillator strengths. The procedure involves the adjustment of Slater parameters so that they determine improved energy levels and eigenvectors. They provide a basis for collision strength calculations in ions where ab initio computations break down or result in reducible errors. This application is demonstrated through modifications of the DISTORTED WAVE collision code and SUPERSTRUCTURE atomic-structure code which interface via a transformation code JAJOM which processes their output. (author)

Computational structural biology: methods and applications

National Research Council Canada - National Science Library

Schwede, Torsten; Peitsch, Manuel Claude

2008-01-01

... sequencing reinforced the observation that structural information is needed to understand the detailed function and mechanism of biological molecules such as enzyme reactions and molecular recognition events. Furthermore, structures are obviously key to the design of molecules with new or improved functions. In this context, computational structural biology...

Structure of Complex Verb Forms in Meiteilon

Directory of Open Access Journals (Sweden)

Lourembam Surjit Singh

2016-12-01

Full Text Available This piece of work proposes to descriptively investigate the structures of complex verbs in Meiteilon. The categorization of such verbs is based on the nature of semantic and syntactic functions of a lexeme or verbal lexeme. A lexeme or verbal lexeme in Meiteilon may have multifunctional properties in the nature of occurrence. Such lexical items can be co-occurred together in a phrase as single functional word. Specifically, in the co-occurrences of two lexical items, the first component of lexical items has different semantic and syntactic functions in comparison to semantic and syntactic functions of the second component of lexical items. Such co-occurrences of two lexical items are the forms of complex verb that are covered with the term complex predicate in this work. The investigation in constructing complex predicate is thoroughly presenting in this work. Keywords: Structures, complex verb, conjunct verb, compound verb, complex predicate

Choosing the Best Enzyme Complex Structure Made Easy.

Science.gov (United States)

Das, Sayoni; Orengo, Christine

2018-04-03

In this issue of Structure, Tyzack et al. (2018) present a study of enzyme-ligand complexes in the PDB and show that the molecular similarity of bound and cognate ligands can be used to choose the most biologically appropriate complex structure for analysis when multiple structures are available. Copyright © 2018 Elsevier Ltd. All rights reserved.

Complex system modelling and control through intelligent soft computations

CERN Document Server

Azar, Ahmad

2015-01-01

The book offers a snapshot of the theories and applications of soft computing in the area of complex systems modeling and control. It presents the most important findings discussed during the 5th International Conference on Modelling, Identification and Control, held in Cairo, from August 31-September 2, 2013. The book consists of twenty-nine selected contributions, which have been thoroughly reviewed and extended before their inclusion in the volume. The different chapters, written by active researchers in the field, report on both current theories and important applications of soft-computing. Besides providing the readers with soft-computing fundamentals, and soft-computing based inductive methodologies/algorithms, the book also discusses key industrial soft-computing applications, as well as multidisciplinary solutions developed for a variety of purposes, like windup control, waste management, security issues, biomedical applications and many others. It is a perfect reference guide for graduate students, r...

Complexity vs energy: theory of computation and theoretical physics

International Nuclear Information System (INIS)

Manin, Y I

2014-01-01

This paper is a survey based upon the talk at the satellite QQQ conference to ECM6, 3Quantum: Algebra Geometry Information, Tallinn, July 2012. It is dedicated to the analogy between the notions of complexity in theoretical computer science and energy in physics. This analogy is not metaphorical: I describe three precise mathematical contexts, suggested recently, in which mathematics related to (un)computability is inspired by and to a degree reproduces formalisms of statistical physics and quantum field theory.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Sener, Melih; Hsin, Jen; Trabuco, Leonardo G.; Villa, Elizabeth; Qian, Pu; Hunter, C. Neil; Schulten, Klaus

2009-01-01

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter (Rba.) sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. The arrangement of the LH1 BChls displays a distortion near the proposed location of the PufX polypeptide. The resulting atomic model for BChl arrays is used to compute the excitonic properties of the dimeric RC-LH1 complex. A comparison is presented between the structural and excitonic features of the S-shaped dimeric BChl array of Rba. sphaeroides and the circular BChl arrangement found in other purple bacteria

Learning Latent Structure in Complex Networks

DEFF Research Database (Denmark)

Mørup, Morten; Hansen, Lars Kai

such as the Modularity, it has recently been shown that latent structure in complex networks is learnable by Bayesian generative link distribution models (Airoldi et al., 2008, Hofman and Wiggins, 2008). In this paper we propose a new generative model that allows representation of latent community structure......Latent structure in complex networks, e.g., in the form of community structure, can help understand network dynamics, identify heterogeneities in network properties, and predict ‘missing’ links. While most community detection algorithms are based on optimizing heuristic clustering objectives...... as in the previous Bayesian approaches and in addition allows learning of node specific link properties similar to that in the modularity objective. We employ a new relaxation method for efficient inference in these generative models that allows us to learn the behavior of very large networks. We compare the link...

General-Purpose Computation with Neural Networks: A Survey of Complexity Theoretic Results

Czech Academy of Sciences Publication Activity Database

Šíma, Jiří; Orponen, P.

2003-01-01

Roč. 15, č. 12 (2003), s. 2727-2778 ISSN 0899-7667 R&D Projects: GA AV ČR IAB2030007; GA ČR GA201/02/1456 Institutional research plan: AV0Z1030915 Keywords : computational power * computational complexity * perceptrons * radial basis functions * spiking neurons * feedforward networks * reccurent networks * probabilistic computation * analog computation Subject RIV: BA - General Mathematics Impact factor: 2.747, year: 2003

Complex network problems in physics, computer science and biology

Science.gov (United States)

Cojocaru, Radu Ionut

There is a close relation between physics and mathematics and the exchange of ideas between these two sciences are well established. However until few years ago there was no such a close relation between physics and computer science. Even more, only recently biologists started to use methods and tools from statistical physics in order to study the behavior of complex system. In this thesis we concentrate on applying and analyzing several methods borrowed from computer science to biology and also we use methods from statistical physics in solving hard problems from computer science. In recent years physicists have been interested in studying the behavior of complex networks. Physics is an experimental science in which theoretical predictions are compared to experiments. In this definition, the term prediction plays a very important role: although the system is complex, it is still possible to get predictions for its behavior, but these predictions are of a probabilistic nature. Spin glasses, lattice gases or the Potts model are a few examples of complex systems in physics. Spin glasses and many frustrated antiferromagnets map exactly to computer science problems in the NP-hard class defined in Chapter 1. In Chapter 1 we discuss a common result from artificial intelligence (AI) which shows that there are some problems which are NP-complete, with the implication that these problems are difficult to solve. We introduce a few well known hard problems from computer science (Satisfiability, Coloring, Vertex Cover together with Maximum Independent Set and Number Partitioning) and then discuss their mapping to problems from physics. In Chapter 2 we provide a short review of combinatorial optimization algorithms and their applications to ground state problems in disordered systems. We discuss the cavity method initially developed for studying the Sherrington-Kirkpatrick model of spin glasses. We extend this model to the study of a specific case of spin glass on the Bethe

Solution structure of the luzopeptin-DNA complex

International Nuclear Information System (INIS)

Zhang, Xiaolu; Patel, D.J.

1991-01-01

The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Once equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. The authors have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The formation of cis peptide bonds for luzopeptin in the complex results in an increased separation of the long sides of the rectangular cyclic depsipeptide backbone and reorients in the glycine amide proton so that it can form an intermolecular hydrogen bond with the 2-carbonyl of T3 in the complex. This observation explains, in part, the requirement for Watson-Crick A·T pairs to be sandwiched between the quinolines at the bisintercalation site in the luzopeptin-DNA complex. The NMR studies on the luzopeptin-d(C-A-T-G) complex unequivocally establish that antitumor agents can undergo conformational transitions on complex formation with DNA, and it is the conformation of the drug in the complex that should serve as the starting point for drug design studies. The above structural details on the solution structure of the luzopeptin-DNA complex also explain the sequence selectivity of luzopeptin for bisintercalation at d(C-A)·d(T-G) steps in the d(C-A-T-G) duplex in solution

Materials-by-design: computation, synthesis, and characterization from atoms to structures

Science.gov (United States)

Yeo, Jingjie; Jung, Gang Seob; Martín-Martínez, Francisco J.; Ling, Shengjie; Gu, Grace X.; Qin, Zhao; Buehler, Markus J.

2018-05-01

In the 50 years that succeeded Richard Feynman’s exposition of the idea that there is ‘plenty of room at the bottom’ for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

Computational methods for structural load and resistance modeling

Science.gov (United States)

Thacker, B. H.; Millwater, H. R.; Harren, S. V.

1991-01-01

An automated capability for computing structural reliability considering uncertainties in both load and resistance variables is presented. The computations are carried out using an automated Advanced Mean Value iteration algorithm (AMV +) with performance functions involving load and resistance variables obtained by both explicit and implicit methods. A complete description of the procedures used is given as well as several illustrative examples, verified by Monte Carlo Analysis. In particular, the computational methods described in the paper are shown to be quite accurate and efficient for a material nonlinear structure considering material damage as a function of several primitive random variables. The results show clearly the effectiveness of the algorithms for computing the reliability of large-scale structural systems with a maximum number of resolutions.

RNA secondary structure prediction using soft computing.

Science.gov (United States)

Ray, Shubhra Sankar; Pal, Sankar K

2013-01-01

Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

Relationships between structural complexity, coral traits, and reef fish assemblages

Science.gov (United States)

Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.

2017-06-01

With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

Counting loop diagrams: computational complexity of higher-order amplitude evaluation

International Nuclear Information System (INIS)

Eijk, E. van; Kleiss, R.; Lazopoulos, A.

2004-01-01

We discuss the computational complexity of the perturbative evaluation of scattering amplitudes, both by the Caravaglios-Moretti algorithm and by direct evaluation of the individual diagrams. For a self-interacting scalar theory, we determine the complexity as a function of the number of external legs. We describe a method for obtaining the number of topologically inequivalent Feynman graphs containing closed loops, and apply this to 1- and 2-loop amplitudes. We also compute the number of graphs weighted by their symmetry factors, thus arriving at exact and asymptotic estimates for the average symmetry factor of diagrams. We present results for the asymptotic number of diagrams up to 10 loops, and prove that the average symmetry factor approaches unity as the number of external legs becomes large. (orig.)

Single neuron computation

CERN Document Server

McKenna, Thomas M; Zornetzer, Steven F

1992-01-01

This book contains twenty-two original contributions that provide a comprehensive overview of computational approaches to understanding a single neuron structure. The focus on cellular-level processes is twofold. From a computational neuroscience perspective, a thorough understanding of the information processing performed by single neurons leads to an understanding of circuit- and systems-level activity. From the standpoint of artificial neural networks (ANNs), a single real neuron is as complex an operational unit as an entire ANN, and formalizing the complex computations performed by real n

Robust inverse scattering full waveform seismic tomography for imaging complex structure

International Nuclear Information System (INIS)

Nurhandoko, Bagus Endar B.; Sukmana, Indriani; Wibowo, Satryo; Deny, Agus; Kurniadi, Rizal; Widowati, Sri; Mubarok, Syahrul; Susilowati; Kaswandhi

2012-01-01

Seismic tomography becomes important tool recently for imaging complex subsurface. It is well known that imaging complex rich fault zone is difficult. In this paper, The application of time domain inverse scattering wave tomography to image the complex fault zone would be shown on this paper, especially an efficient time domain inverse scattering tomography and their run in cluster parallel computer which has been developed. This algorithm is purely based on scattering theory through solving Lippmann Schwienger integral by using Born's approximation. In this paper, it is shown the robustness of this algorithm especially in avoiding the inversion trapped in local minimum to reach global minimum. A large data are solved by windowing and blocking technique of memory as well as computation. Parameter of windowing computation is based on shot gather's aperture. This windowing technique reduces memory as well as computation significantly. This parallel algorithm is done by means cluster system of 120 processors from 20 nodes of AMD Phenom II. Benchmarking of this algorithm is done by means Marmoussi model which can be representative of complex rich fault area. It is shown that the proposed method can image clearly the rich fault and complex zone in Marmoussi model even though the initial model is quite far from the true model. Therefore, this method can be as one of solution to image the very complex mode.

Robust inverse scattering full waveform seismic tomography for imaging complex structure

Energy Technology Data Exchange (ETDEWEB)

Nurhandoko, Bagus Endar B.; Sukmana, Indriani; Wibowo, Satryo; Deny, Agus; Kurniadi, Rizal; Widowati, Sri; Mubarok, Syahrul; Susilowati; Kaswandhi [Wave Inversion and Subsurface Fluid Imaging Research (WISFIR) Lab., Complex System Research Division, Physics Department, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung. and Rock Fluid Imaging Lab., Rock Physics and Cluster C (Indonesia); Rock Fluid Imaging Lab., Rock Physics and Cluster Computing Center, Bandung (Indonesia); Physics Department of Institut Teknologi Bandung (Indonesia); Rock Fluid Imaging Lab., Rock Physics and Cluster Computing Center, Bandung, Indonesia and Institut Teknologi Telkom, Bandung (Indonesia); Rock Fluid Imaging Lab., Rock Physics and Cluster Computing Center, Bandung (Indonesia)

2012-06-20

Seismic tomography becomes important tool recently for imaging complex subsurface. It is well known that imaging complex rich fault zone is difficult. In this paper, The application of time domain inverse scattering wave tomography to image the complex fault zone would be shown on this paper, especially an efficient time domain inverse scattering tomography and their run in cluster parallel computer which has been developed. This algorithm is purely based on scattering theory through solving Lippmann Schwienger integral by using Born's approximation. In this paper, it is shown the robustness of this algorithm especially in avoiding the inversion trapped in local minimum to reach global minimum. A large data are solved by windowing and blocking technique of memory as well as computation. Parameter of windowing computation is based on shot gather's aperture. This windowing technique reduces memory as well as computation significantly. This parallel algorithm is done by means cluster system of 120 processors from 20 nodes of AMD Phenom II. Benchmarking of this algorithm is done by means Marmoussi model which can be representative of complex rich fault area. It is shown that the proposed method can image clearly the rich fault and complex zone in Marmoussi model even though the initial model is quite far from the true model. Therefore, this method can be as one of solution to image the very complex mode.

Metal-induced gap states in ferroelectric capacitors and its relationship with complex band structures

Science.gov (United States)

Junquera, Javier; Aguado-Puente, Pablo

2013-03-01

At metal-isulator interfaces, the metallic wave functions with an energy eigenvalue within the band gap decay exponentially inside the dielectric (metal-induced gap states, MIGS). These MIGS can be actually regarded as Bloch functions with an associated complex wave vector. Usually only real values of the wave vectors are discussed in text books, since infinite periodicity is assumed and, in that situation, wave functions growing exponentially in any direction would not be physically valid. However, localized wave functions with an exponential decay are indeed perfectly valid solution of the Schrodinger equation in the presence of defects, surfaces or interfaces. For this reason, properties of MIGS have been typically discussed in terms of the complex band structure of bulk materials. The probable dependence on the interface particulars has been rarely taken into account explicitly due to the difficulties to include them into the model or simulations. We aim to characterize from first-principles simulations the MIGS in realistic ferroelectric capacitors and their connection with the complex band structure of the ferroelectric material. We emphasize the influence of the real interface beyond the complex band structure of bulk materials. Financial support provided by MICINN Grant FIS2009-12721-C04-02, and by the European Union Grant No. CP-FP 228989-2 ``OxIDes''. Computer resources provided by the RES.

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

Energy Technology Data Exchange (ETDEWEB)

Hadjidoukas, P.E.; Angelikopoulos, P. [Computational Science and Engineering Laboratory, ETH Zürich, CH-8092 (Switzerland); Papadimitriou, C. [Department of Mechanical Engineering, University of Thessaly, GR-38334 Volos (Greece); Koumoutsakos, P., E-mail: petros@ethz.ch [Computational Science and Engineering Laboratory, ETH Zürich, CH-8092 (Switzerland)

2015-03-01

We present Π4U,{sup 1} an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

The complex band structure for armchair graphene nanoribbons

International Nuclear Information System (INIS)

Zhang Liu-Jun; Xia Tong-Sheng

2010-01-01

Using a tight binding transfer matrix method, we calculate the complex band structure of armchair graphene nanoribbons. The real part of the complex band structure calculated by the transfer matrix method fits well with the bulk band structure calculated by a Hermitian matrix. The complex band structure gives extra information on carrier's decay behaviour. The imaginary loop connects the conduction and valence band, and can profoundly affect the characteristics of nanoscale electronic device made with graphene nanoribbons. In this work, the complex band structure calculation includes not only the first nearest neighbour interaction, but also the effects of edge bond relaxation and the third nearest neighbour interaction. The band gap is classified into three classes. Due to the edge bond relaxation and the third nearest neighbour interaction term, it opens a band gap for N = 3M − 1. The band gap is almost unchanged for N = 3M + 1, but decreased for N = 3M. The maximum imaginary wave vector length provides additional information about the electrical characteristics of graphene nanoribbons, and is also classified into three classes

Computational complexity and memory usage for multi-frontal direct solvers used in p finite element analysis

KAUST Repository

Calo, Victor M.; Collier, Nathan; Pardo, David; Paszyński, Maciej R.

2011-01-01

The multi-frontal direct solver is the state of the art for the direct solution of linear systems. This paper provides computational complexity and memory usage estimates for the application of the multi-frontal direct solver algorithm on linear systems resulting from p finite elements. Specifically we provide the estimates for systems resulting from C0 polynomial spaces spanned by B-splines. The structured grid and uniform polynomial order used in isogeometric meshes simplifies the analysis.

Computational complexity and memory usage for multi-frontal direct solvers used in p finite element analysis

KAUST Repository

Calo, Victor M.

2011-05-14

The multi-frontal direct solver is the state of the art for the direct solution of linear systems. This paper provides computational complexity and memory usage estimates for the application of the multi-frontal direct solver algorithm on linear systems resulting from p finite elements. Specifically we provide the estimates for systems resulting from C0 polynomial spaces spanned by B-splines. The structured grid and uniform polynomial order used in isogeometric meshes simplifies the analysis.

Electronic Structure of Transition Metal Clusters, Actinide Complexes and Their Reactivities

Energy Technology Data Exchange (ETDEWEB)

Krishnan Balasubramanian

2009-07-18

This is a continuing DOE-BES funded project on transition metal and actinide containing species, aimed at the electronic structure and spectroscopy of transition metal and actinide containing species. While a long term connection of these species is to catalysis and environmental management of high-level nuclear wastes, the immediate relevance is directly to other DOE-BES funded experimental projects at DOE-National labs and universities. There are a number of ongoing gas-phase spectroscopic studies of these species at various places, and our computational work has been inspired by these experimental studies and we have also inspired other experimental and theoretical studies. Thus our studies have varied from spectroscopy of diatomic transition metal carbides to large complexes containing transition metals, and actinide complexes that are critical to the environment. In addition, we are continuing to make code enhancements and modernization of ALCHEMY II set of codes and its interface with relativistic configuration interaction (RCI). At present these codes can carry out multi-reference computations that included up to 60 million configurations and multiple states from each such CI expansion. ALCHEMY II codes have been modernized and converted to a variety of platforms such as Windows XP, and Linux. We have revamped the symbolic CI code to automate the MRSDCI technique so that the references are automatically chosen with a given cutoff from the CASSCF and thus we are doing accurate MRSDCI computations with 10,000 or larger reference space of configurations. The RCI code can also handle a large number of reference configurations, which include up to 10,000 reference configurations. Another major progress is in routinely including larger basis sets up to 5g functions in thee computations. Of course higher angular momenta functions can also be handled using Gaussian and other codes with other methods such as DFT, MP2, CCSD(T), etc. We have also calibrated our RECP

Electronic Structure of Transition Metal Clusters, Actinide Complexes and Their Reactivities

International Nuclear Information System (INIS)

Balasubramanian, Krishnan

2009-01-01

This is a continuing DOE-BES funded project on transition metal and actinide containing species, aimed at the electronic structure and spectroscopy of transition metal and actinide containing species. While a long term connection of these species is to catalysis and environmental management of high-level nuclear wastes, the immediate relevance is directly to other DOE-BES funded experimental projects at DOE-National labs and universities. There are a number of ongoing gas-phase spectroscopic studies of these species at various places, and our computational work has been inspired by these experimental studies and we have also inspired other experimental and theoretical studies. Thus our studies have varied from spectroscopy of diatomic transition metal carbides to large complexes containing transition metals, and actinide complexes that are critical to the environment. In addition, we are continuing to make code enhancements and modernization of ALCHEMY II set of codes and its interface with relativistic configuration interaction (RCI). At present these codes can carry out multi-reference computations that included up to 60 million configurations and multiple states from each such CI expansion. ALCHEMY II codes have been modernized and converted to a variety of platforms such as Windows XP, and Linux. We have revamped the symbolic CI code to automate the MRSDCI technique so that the references are automatically chosen with a given cutoff from the CASSCF and thus we are doing accurate MRSDCI computations with 10,000 or larger reference space of configurations. The RCI code can also handle a large number of reference configurations, which include up to 10,000 reference configurations. Another major progress is in routinely including larger basis sets up to 5g functions in thee computations. Of course higher angular momenta functions can also be handled using Gaussian and other codes with other methods such as DFT, MP2, CCSD(T), etc. We have also calibrated our RECP

Computed tomography of von Meyenburg complex simulating micro-abscesses

International Nuclear Information System (INIS)

Sada, P.N.; Ramakrishna, B.

1994-01-01

A case is presented of a bile duct hamartoma in a 44 year old man being evaluated for abdominal pain. The computed tomography (CT) findings suggested micro-abscesses in the liver and a CT guided tru-cut biopsy showed von Meyenburg complex. 9 refs., 3 figs

77 FR 50726 - Software Requirement Specifications for Digital Computer Software and Complex Electronics Used in...

Science.gov (United States)

2012-08-22

... Computer Software and Complex Electronics Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear...-1209, ``Software Requirement Specifications for Digital Computer Software and Complex Electronics used... Electronics Engineers (ANSI/IEEE) Standard 830-1998, ``IEEE Recommended Practice for Software Requirements...

A computationally efficient simulator for three-dimensional Monte Carlo simulation of ion implantation into complex structures

International Nuclear Information System (INIS)

Li Di; Wang Geng; Chen Yang; Li Lin; Shrivastav, Gaurav; Oak, Stimit; Tasch, Al; Banerjee, Sanjay; Obradovic, Borna

2001-01-01

A physically-based three-dimensional Monte Carlo simulator has been developed within UT-MARLOWE, which is capable of simulating ion implantation into multi-material systems and arbitrary topography. Introducing the third dimension can result in a severe CPU time penalty. In order to minimize this penalty, a three-dimensional trajectory replication algorithm has been developed, implemented and verified. More than two orders of magnitude savings of CPU time have been observed. An unbalanced Octree structure was used to decompose three-dimensional structures. It effectively simplifies the structure, offers a good balance between modeling accuracy and computational efficiency, and allows arbitrary precision of mapping the Octree onto desired structure. Using the well-established and validated physical models in UT-MARLOWE 5.0, this simulator has been extensively verified by comparing the integrated one-dimensional simulation results with secondary ion mass spectroscopy (SIMS). Two options, the typical case and the worst scenario, have been selected to simulate ion implantation into poly-silicon under various scenarios using this simulator: implantation into a random, amorphous network, and implantation into the worst-case channeling condition, into (1 1 0) orientated wafers

Fast and accurate algorithm for the computation of complex linear canonical transforms.

Science.gov (United States)

Koç, Aykut; Ozaktas, Haldun M; Hesselink, Lambertus

2010-09-01

A fast and accurate algorithm is developed for the numerical computation of the family of complex linear canonical transforms (CLCTs), which represent the input-output relationship of complex quadratic-phase systems. Allowing the linear canonical transform parameters to be complex numbers makes it possible to represent paraxial optical systems that involve complex parameters. These include lossy systems such as Gaussian apertures, Gaussian ducts, or complex graded-index media, as well as lossless thin lenses and sections of free space and any arbitrary combinations of them. Complex-ordered fractional Fourier transforms (CFRTs) are a special case of CLCTs, and therefore a fast and accurate algorithm to compute CFRTs is included as a special case of the presented algorithm. The algorithm is based on decomposition of an arbitrary CLCT matrix into real and complex chirp multiplications and Fourier transforms. The samples of the output are obtained from the samples of the input in approximately N log N time, where N is the number of input samples. A space-bandwidth product tracking formalism is developed to ensure that the number of samples is information-theoretically sufficient to reconstruct the continuous transform, but not unnecessarily redundant.

Radical bonding: structure and stability of bis(phenalenyl) complexes of divalent metals from across the periodic table.

Science.gov (United States)

Craciun, Smaranda; Donald, Kelling J

2009-07-06

We examine the bonding possibilities of the bis(phenalenyl) MP(2) sandwich complexes of the divalent metals M = Be, Mg, Ca, Sr, Ba, Zn, Cd, and Hg, at the B3LYP level of theory. The outcome is an extraordinarily diverse class of low symmetry bis(phenalenyl)metal complexes in which bonding preferences and binding enthalpies differ dramatically. The lowest energy group 2 metal MP(2) complexes include an intriguing eta(1),eta(3) BeP(2) structure, and bent eta(6),eta(6) systems for M = Ca, Sr, and Ba. The group 12 bis(phenalenyl) complexes are thermodynamically unstable eta(1),eta(1) slip-sandwich structures. To better understand changes in the structural preferences going from the (eta(6),eta(6)) group 2 to the (eta(1),eta(1)) group 12 complexes, we explored the bonding in the bis(phenalenyl) complexes of transition metals with stable +2 oxidations states between Ca and Zn in period 4. The computed binding enthalpies are large and negative for nearly all of the minimum energy bis(phenalenyl) complexes of the group 2 and the transition metals; they are tiny for MgP(2), and are quite positive for the group 12 systems. The structural preferences and stability of the complexes is a subtle negotiation of several influences: the (un)availability of (n - 1)d and np, orbitals for bonding, the cost of the rehybridization at carbon sites in the phenalenyl rings in preparation for bonding to the metals, and the (P---P) interaction between the phenalenyl radicals.

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

Directory of Open Access Journals (Sweden)

Huiying Zhao

Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

The information exchange between moduluses in the system of module programming of the computation complexes

International Nuclear Information System (INIS)

Zinin, A.I.; Kolesov, V.E.; Nevinitsa, A.I.

1975-01-01

The report contains description of the method of construction of computer programs complexes for computation purposes for M-220 computers using the ALGOL-60 code for programming. The complex is organised on the modulus system principle and can include substantial number of modulus programs. The information exchange between separate moduli is done by means of special interpreting program and the information unit exchanged is a specially arranged file of data. For addressing to the interpreting program in the ALGOL-60 frameworks small number of specially created procedure-codes is used. The method proposed gives possibilities to program separate moduli of the complex independently and to expand the complex if necessary. In this case separate moduli or groups of moduli depending on the method of segmentation of the general problem solved by the complex will be of the independent interest and could be used out of the complex as traditional programs. (author)

Exact complexity: The spectral decomposition of intrinsic computation

International Nuclear Information System (INIS)

Crutchfield, James P.; Ellison, Christopher J.; Riechers, Paul M.

2016-01-01

We give exact formulae for a wide family of complexity measures that capture the organization of hidden nonlinear processes. The spectral decomposition of operator-valued functions leads to closed-form expressions involving the full eigenvalue spectrum of the mixed-state presentation of a process's ϵ-machine causal-state dynamic. Measures include correlation functions, power spectra, past-future mutual information, transient and synchronization informations, and many others. As a result, a direct and complete analysis of intrinsic computation is now available for the temporal organization of finitary hidden Markov models and nonlinear dynamical systems with generating partitions and for the spatial organization in one-dimensional systems, including spin systems, cellular automata, and complex materials via chaotic crystallography. - Highlights: • We provide exact, closed-form expressions for a hidden stationary process' intrinsic computation. • These include information measures such as the excess entropy, transient information, and synchronization information and the entropy-rate finite-length approximations. • The method uses an epsilon-machine's mixed-state presentation. • The spectral decomposition of the mixed-state presentation relies on the recent development of meromorphic functional calculus for nondiagonalizable operators.

Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

DEFF Research Database (Denmark)

Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen

2010-01-01

, and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set includes both...... substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 kJ/mol. Subsequent......Predicting binding affinities for receptor-ligand complexes is still one of the challenging processes in computational structure-based ligand design. Many computational methods have been developed to achieve this goal, such as docking and scoring methods, the linear interaction energy (LIE) method...

Accurate Computed Enthalpies of Spin Crossover in Iron and Cobalt Complexes

DEFF Research Database (Denmark)

Kepp, Kasper Planeta; Cirera, J

2009-01-01

Despite their importance in many chemical processes, the relative energies of spin states of transition metal complexes have so far been haunted by large computational errors. By the use of six functionals, B3LYP, BP86, TPSS, TPSSh, M06L, and M06L, this work studies nine complexes (seven with iron...

Post-structuralism, Complexity and Poetics.

OpenAIRE

Dillon, Michael

2000-01-01

Post-structuralism and complexity are plural and diverse modes of thought that share a common subscription to the �anteriority of radical relationality�. They nonetheless subscribe to a different ethic of life because they address the anteriority of radical relationality in different ways. Complexity remains strategic in its bid to become a power-knowledge of the laws of becoming. It derives that strategic ethic from its scientific interest in the implicate order of non-linearity that is ...

Student Computer Use: Its Organizational Structure and Institutional Support.

Science.gov (United States)

Juska, Arunas; Paris, Arthur E.

1993-01-01

Examines the structure of undergraduate computing at a large private university, including patterns of use, impact of computer ownership and gender, and the bureaucratic structure in which usage is embedded. The profile of computer use uncovered in a survey is compared with reports offered by the institution and the trade press. (10 references)…

Computational Analysis of SAXS Data Acquisition.

Science.gov (United States)

Dong, Hui; Kim, Jin Seob; Chirikjian, Gregory S

2015-09-01

Small-angle x-ray scattering (SAXS) is an experimental biophysical method used for gaining insight into the structure of large biomolecular complexes. Under appropriate chemical conditions, the information obtained from a SAXS experiment can be equated to the pair distribution function, which is the distribution of distances between every pair of points in the complex. Here we develop a mathematical model to calculate the pair distribution function for a structure of known density, and analyze the computational complexity of these calculations. Efficient recursive computation of this forward model is an important step in solving the inverse problem of recovering the three-dimensional density of biomolecular structures from their pair distribution functions. In particular, we show that integrals of products of three spherical-Bessel functions arise naturally in this context. We then develop an algorithm for the efficient recursive computation of these integrals.

Group actions, non-Kähler complex manifolds and SKT structures

Directory of Open Access Journals (Sweden)

Poddar Mainak

2018-02-01

Full Text Available We give a construction of integrable complex structures on the total space of a smooth principal bundle over a complex manifold, with an even dimensional compact Lie group as structure group, under certain conditions. This generalizes the constructions of complex structure on compact Lie groups by Samelson and Wang, and on principal torus bundles by Calabi-Eckmann and others. It also yields large classes of new examples of non-Kähler compact complex manifolds. Moreover, under suitable restrictions on the base manifold, the structure group, and characteristic classes, the total space of the principal bundle admits SKT metrics. This generalizes recent results of Grantcharov et al. We study the Picard group and the algebraic dimension of the total space in some cases. We also use a slightly generalized version of the construction to obtain (non-Kähler complex structures on tangential frame bundles of complex orbifolds.

Intraoperative computed tomography with an integrated navigation system in stabilization surgery for complex craniovertebral junction malformation.

Science.gov (United States)

Yu, Xinguang; Li, Lianfeng; Wang, Peng; Yin, Yiheng; Bu, Bo; Zhou, Dingbiao

2014-07-01

This study was designed to report our preliminary experience with stabilization procedures for complex craniovertebral junction malformation (CVJM) using intraoperative computed tomography (iCT) with an integrated neuronavigation system (NNS). To evaluate the workflow, feasibility and clinical outcome of stabilization procedures using iCT image-guided navigation for complex CVJM. The stabilization procedures in CVJM are complex because of the area's intricate geometry and bony structures, its critical relationship to neurovascular structures and the intricate biomechanical issues involved. A sliding gantry 40-slice computed tomography scanner was installed in a preexisting operating room. The images were transferred directly from the scanner to the NNS using an automated registration system. On the basis of the analysis of intraoperative computed tomographic images, 23 cases (11 males, 12 females) with complicated CVJM underwent navigated stabilization procedures to allow more control over screw placement. The age of these patients were 19-52 years (mean: 33.5 y). We performed C1-C2 transarticular screw fixation in 6 patients to produce atlantoaxial arthrodesis with better reliability. Because of a high-riding transverse foramen on at least 1 side of the C2 vertebra and an anomalous vertebral artery position, 7 patients underwent C1 lateral mass and C2 pedicle screw fixation. Ten additional patients were treated with individualized occipitocervical fixation surgery from the hypoplasia of C1 or constraints due to C2 bone structure. In total, 108 screws were inserted into 23 patients using navigational assistance. The screws comprised 20 C1 lateral mass screws, 26 C2, 14 C3, or 4 C4 pedicle screws, 32 occipital screws, and 12 C1-C2 transarticular screws. There were no vascular or neural complications except for pedicle perforations that were detected in 2 (1.9%) patients and were corrected intraoperatively without any persistent nerves or vessel damage. The overall

Quantum chemical studies on electronic structure and photodynamics of ruthenium complexes

International Nuclear Information System (INIS)

Freitag, L.

2015-01-01

Ruthenium complexes have found their way into many applications in the last decades. Among those, ruthenium polypyridyl compounds have been employed as light harvesting devices and photosensitisers in artificial photosynthesis and molecular photocatalysis. Ruthenium nitrosyl complexes are rapidly emerging as NO delivery agents to biological tissues with promising applications in anticancer photodynamic therapy, thanks to their ability to photorelease nitric oxide (NO). This thesis encompasses computational studies on reactivity, electronic structure, excited states and photodynamics of several ruthenium nitrosyl and polypyridyl complexes. The first part of the thesis deals with ruthenium nitrosyls. The cis-trans isomerisation mechanism of RuHIndNO, a ruthenium nitrosyl derivate of the prominent anti-cancer drug candidate KP1019, is investigated with density functional theory calculations. Next, the electronic structure of the ground and the first excited triplet state of RuHIndNO is studied with multiconfigurational methods including the density-matrix renormalisation group (DMRG). The obtained multiconfigurational wavefunctions and DMRG-based orbital entanglement analysis provides theoretical insight into the non-innocence of the NO ligand in nitrosyl complexes by describing the electron correlation in the Ru--NO bond and assigning oxidation states to the metal and the NO ligand. Another study is performed on excited states of ruthenium nitrosyl complexes with quantum chemical calculations and surface-hopping dynamics to obtain insights into the photodissociation mechanism of NO. The second part of this thesis is devoted to the excited states and photophysics of ruthenium polypyridyl complexes. Accurate excitation energies of tris(2,2-bipyridine)ruthenium (II), the prototype ruthenium polypyridyl are obtained with multiconfigurational calculations assisted by an orbital entanglement analysis. Subsequently, the effect of the ligand substitution on the photophysics

Thermodynamic and structural properties in complexing media

International Nuclear Information System (INIS)

Di Giandomenico, M.V.

2007-10-01

Protactinium is experiencing a renewal of interest in the frame of long-term energy production. Modelling the behaviour of this element in the geosphere requires thermodynamic and structural data relevant to environmental conditions. Now deep clayey formation are considered for the disposal of radioactive waste and high values of natural sulphate contents have been determined in pore water in equilibrium with clay surface. Because of its tendency to polymerisation, hydrolysis and sorption on all solid supports, the equilibria constants relative to monomer species were determined at tracer scale (ca. 10 - 12 M) with 233 Pa. The complexation constants of Pa(V) and sulphate ions were calculated starting from a systematic study of the apparent distribution coefficient D in the system TTA/Toluene/H 2 O/Na 2 SO 4 /HClO 4 /NaClO 4 and as a function of ionic strength, temperature, free sulphate, protons and chelatant concentration. First of all, the interaction between free species H + , SO 4 - , Na + leads to the formation of HSO 4 - and NaSO 4 - , for which concentrations depend upon the related thermodynamic constants. For this purpose a computer code was developed in order to determine all free species concentration. This iterative code takes into account the influence of temperature and ionic strength (SIT modelling) on thermodynamic constants. The direct measure of Pa(V) in the organic and aqueous phase by g-spectrometry had conducted to estimate the apparent distribution coefficient D as function of free sulphate ions. Complexation constants have been determined after a mathematical treatment of D. The extrapolation of these constants at zero ionic strength have been realized by SIT modelling at different temperatures. Besides, enthalpy and entropy values were calculated. Parallelly, the structural study of Pa(V) was performed using 231 Pa. XANES and EXAFS spectra show unambiguously the absence of the trans di-oxo bond that characterizes the other early actinide

Single photon emission computed tomography in AIDS dementia complex

International Nuclear Information System (INIS)

Pohl, P.; Vogl, G.; Fill, H.; Roessler, H.Z.; Zangerle, R.; Gerstenbrand, F.

1988-01-01

Single photon emission computed tomography (SPECT) studies were performed in AIDS dementia complex using IMP in 12 patients (and HM-PAO in four of these same patients). In all patients, SPECT revealed either multiple or focal uptake defects, the latter corresponding with focal signs or symptoms in all but one case. Computerized tomography showed a diffuse cerebral atrophy in eight of 12 patients, magnetic resonance imaging exhibited changes like atrophy and/or leukoencephalopathy in two of five cases. Our data indicate that both disturbance of cerebral amine metabolism and alteration of local perfusion share in the pathogenesis of AIDS dementia complex. SPECT is an important aid in the diagnosis of AIDS dementia complex and contributes to the understanding of the pathophysiological mechanisms of this disorder

Structured brain computing and its learning

International Nuclear Information System (INIS)

Ae, Tadashi; Araki, Hiroyuki; Sakai, Keiichi

1999-01-01

We have proposed a two-level architecture for brain computing, where two levels are introduced for processing of meta-symbol. At level 1 a conventional pattern recognition is performed, where neural computation is included, and its output gives the meta-symbol which is a symbol enlarged from a symbol to a kind of pattern. At Level 2 an algorithm acquisition is made by using a machine for abstract states. We are also developing the VLSI chips at each level for SBC (Structured Brain Computer) Ver.1.0

Stochastic transport through complex comb structures

International Nuclear Information System (INIS)

Zaburdaev, V. Yu.; Popov, P. V.; Romanov, A. S.; Chukbar, K. V.

2008-01-01

A unified rigorous approach is used to derive fractional differential equations describing subdiffusive transport through comb structures of various geometrical complexity. A general nontrivial effect of the initial particle distribution on the subsequent evolution is exposed. Solutions having qualitative features of practical importance are given for joined structures with widely different fractional exponents

Digital computer structure and design

CERN Document Server

Townsend, R

2014-01-01

Digital Computer Structure and Design, Second Edition discusses switching theory, counters, sequential circuits, number representation, and arithmetic functions The book also describes computer memories, the processor, data flow system of the processor, the processor control system, and the input-output system. Switching theory, which is purely a mathematical concept, centers on the properties of interconnected networks of ""gates."" The theory deals with binary functions of 1 and 0 which can change instantaneously from one to the other without intermediate values. The binary number system is

Multiscale modeling of complex molecular structure and dynamics with MBN Explorer

CERN Document Server

Solov’yov, Ilia A; Solov’yov, Andrey V

2017-01-01

This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the meso-scale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potenti...

Compact complex surfaces with geometric structures related to split quaternions

International Nuclear Information System (INIS)

Davidov, Johann; Grantcharov, Gueo; Mushkarov, Oleg; Yotov, Miroslav

2012-01-01

We study the problem of existence of geometric structures on compact complex surfaces that are related to split quaternions. These structures, called para-hypercomplex, para-hyperhermitian and para-hyperkähler, are analogs of the hypercomplex, hyperhermitian and hyperkähler structures in the definite case. We show that a compact 4-manifold carries a para-hyperkähler structure iff it has a metric of split signature together with two parallel, null, orthogonal, pointwise linearly independent vector fields. Every compact complex surface admitting a para-hyperhermitian structure has vanishing first Chern class and we show that, unlike the definite case, many of these surfaces carry infinite-dimensional families of such structures. We provide also compact examples of complex surfaces with para-hyperhermitian structures which are not locally conformally para-hyperkähler. Finally, we discuss the problem of non-existence of para-hyperhermitian structures on Inoue surfaces of type S 0 and provide a list of compact complex surfaces which could carry para-hypercomplex structures.

Computing Hypercrossed Complex Pairings in Digital Images

Directory of Open Access Journals (Sweden)

Simge Öztunç

2013-01-01

Full Text Available We consider an additive group structure in digital images and introduce the commutator in digital images. Then we calculate the hypercrossed complex pairings which generates a normal subgroup in dimension 2 and in dimension 3 by using 8-adjacency and 26-adjacency.

Modelling the structure of complex networks

DEFF Research Database (Denmark)

Herlau, Tue

networks has been independently studied as mathematical objects in their own right. As such, there has been both an increased demand for statistical methods for complex networks as well as a quickly growing mathematical literature on the subject. In this dissertation we explore aspects of modelling complex....... The next chapters will treat some of the various symmetries, representer theorems and probabilistic structures often deployed in the modelling complex networks, the construction of sampling methods and various network models. The introductory chapters will serve to provide context for the included written...

Several problems of algorithmization in integrated computation programs on third generation computers for short circuit currents in complex power networks

Energy Technology Data Exchange (ETDEWEB)

Krylov, V.A.; Pisarenko, V.P.

1982-01-01

Methods of modeling complex power networks with short circuits in the networks are described. The methods are implemented in integrated computation programs for short circuit currents and equivalents in electrical networks with a large number of branch points (up to 1000) on a computer with a limited on line memory capacity (M equals 4030 for the computer).

Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

Science.gov (United States)

Bae, Juhee; Watson, Benjamin

2014-12-01

In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

Multilayer Stochastic Block Models Reveal the Multilayer Structure of Complex Networks

Directory of Open Access Journals (Sweden)

Toni Vallès-Català

2016-03-01

Full Text Available In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these studies assume that the interactions between systems components in each one of the layers are known, while typically for real-world systems we do not have that information. Here, we address the issue of uncovering the different interaction layers from aggregate data by introducing multilayer stochastic block models (SBMs, a generalization of single-layer SBMs that considers different mechanisms of layer aggregation. First, we find the complete probabilistic solution to the problem of finding the optimal multilayer SBM for a given aggregate-observed network. Because this solution is computationally intractable, we propose an approximation that enables us to verify that multilayer SBMs are more predictive of network structure in real-world complex systems.

Wireless Mobile Computing and its Links to Descriptive Complexity

Czech Academy of Sciences Publication Activity Database

Wiedermann, Jiří; Pardubská, D.

2008-01-01

Roč. 19, č. 4 (2008), s. 887-913 ISSN 0129-0541 R&D Projects: GA AV ČR 1ET100300517 Institutional research plan: CEZ:AV0Z10300504 Keywords : alternating Turing machine * simulation * simultaneous time-space complexity * wireless parallel Turing machine Subject RIV: IN - Informatics, Computer Science Impact factor: 0.554, year: 2008

Structural and computational aspects of simple and influence games

OpenAIRE

Riquelme Csori, Fabián

2014-01-01

Simple games are a fundamental class of cooperative games. They have a huge relevance in several areas of computer science, social sciences and discrete applied mathematics. The algorithmic and computational complexity aspects of simple games have been gaining notoriety in the recent years. In this thesis we review different computational problems related to properties, parameters, and solution concepts of simple games. We consider different forms of representation of simple games, regular...

Computer simulation of complexity in plasmas

International Nuclear Information System (INIS)

Hayashi, Takaya; Sato, Tetsuya

1998-01-01

By making a comprehensive comparative study of many self-organizing phenomena occurring in magnetohydrodynamics and kinetic plasmas, we came up with a hypothetical grand view of self-organization. This assertion is confirmed by a recent computer simulation for a broader science field, specifically, the structure formation of short polymer chains, where the nature of the interaction is completely different from that of plasmas. It is found that the formation of the global orientation order proceeds stepwise. (author)

Structural insights into transcription complexes

NARCIS (Netherlands)

Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

2011-01-01

Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

The Use of Hebbian Cell Assemblies for Nonlinear Computation

DEFF Research Database (Denmark)

Tetzlaff, Christian; Dasgupta, Sakyasingha; Kulvicius, Tomas

2015-01-01

When learning a complex task our nervous system self-organizes large groups of neurons into coherent dynamic activity patterns. During this, a network with multiple, simultaneously active, and computationally powerful cell assemblies is created. How such ordered structures are formed while preser...... computing complex non-linear transforms and - for execution - must cooperate with each other without interference. This mechanism, thus, permits the self-organization of computationally powerful sub-structures in dynamic networks for behavior control....

Complex computation in the retina

Science.gov (United States)

Deshmukh, Nikhil Rajiv

Elucidating the general principles of computation in neural circuits is a difficult problem requiring both a tractable model circuit as well as sophisticated measurement tools. This thesis advances our understanding of complex computation in the salamander retina and its underlying circuitry and furthers the development of advanced tools to enable detailed study of neural circuits. The retina provides an ideal model system for neural circuits in general because it is capable of producing complex representations of the visual scene, and both its inputs and outputs are accessible to the experimenter. Chapter 2 describes the biophysical mechanisms that give rise to the omitted stimulus response in retinal ganglion cells described in Schwartz et al., (2007) and Schwartz and Berry, (2008). The extra response to omitted flashes is generated at the input to bipolar cells, and is separable from the characteristic latency shift of the OSR apparent in ganglion cells, which must occur downstream in the circuit. Chapter 3 characterizes the nonlinearities at the first synapse of the ON pathway in response to high contrast flashes and develops a phenomenological model that captures the effect of synaptic activation and intracellular signaling dynamics on flash responses. This work is the first attempt to model the dynamics of the poorly characterized mGluR6 transduction cascade unique to ON bipolar cells, and explains the second lobe of the biphasic flash response. Complementary to the study of neural circuits, recent advances in wafer-scale photolithography have made possible new devices to measure the electrical and mechanical properties of neurons. Chapter 4 reports a novel piezoelectric sensor that facilitates the simultaneous measurement of electrical and mechanical signals in neural tissue. This technology could reveal the relationship between the electrical activity of neurons and their local mechanical environment, which is critical to the study of mechanoreceptors

Structure of a complex of uridine phosphorylase from Yersinia pseudotuberculosis with the modified bacteriostatic antibacterial drug determined by X-ray crystallography and computer analysis

Energy Technology Data Exchange (ETDEWEB)

Balaev, V. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com; Gabdoulkhakov, A. G.; Seregina, T. A.; Dontsova, M. V.; Mikhailov, A. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2015-03-15

Pseudotuberculosis and bubonic plague are acute infectious diseases caused by the bacteria Yersinia pseudotuberculosis and Yersinia pestis. These diseases are treated, in particular, with trimethoprim and its modified analogues. However, uridine phosphorylases (pyrimidine nucleoside phosphorylases) that are present in bacterial cells neutralize the action of trimethoprim and its modified analogues on the cells. In order to reveal the character of the interaction of the drug with bacterial uridine phosphorylase, the atomic structure of the unligated molecule of uridine-specific pyrimidine nucleoside phosphorylase from Yersinia pseudotuberculosis (YptUPh) was determined by X-ray diffraction at 1.7 Å resolution with high reliability (R{sub work} = 16.2, R{sub free} = 19.4%; r.m.s.d. of bond lengths and bond angles are 0.006 Å and 1.005°, respectively; DPI = 0.107 Å). The atoms of the amino acid residues of the functionally important secondary-structure elements—the loop L9 and the helix H8—of the enzyme YptUPh were located. The three-dimensional structure of the complex of YptUPh with modified trimethoprim—referred to as 53I—was determined by the computer simulation. It was shown that 53I is a pseudosubstrate of uridine phosphorylases, and its pyrimidine-2,4-diamine group is located in the phosphate-binding site of the enzyme YptUPh.

Structure of a complex of uridine phosphorylase from Yersinia pseudotuberculosis with the modified bacteriostatic antibacterial drug determined by X-ray crystallography and computer analysis

International Nuclear Information System (INIS)

Balaev, V. V.; Lashkov, A. A.; Gabdoulkhakov, A. G.; Seregina, T. A.; Dontsova, M. V.; Mikhailov, A. M.

2015-01-01

Pseudotuberculosis and bubonic plague are acute infectious diseases caused by the bacteria Yersinia pseudotuberculosis and Yersinia pestis. These diseases are treated, in particular, with trimethoprim and its modified analogues. However, uridine phosphorylases (pyrimidine nucleoside phosphorylases) that are present in bacterial cells neutralize the action of trimethoprim and its modified analogues on the cells. In order to reveal the character of the interaction of the drug with bacterial uridine phosphorylase, the atomic structure of the unligated molecule of uridine-specific pyrimidine nucleoside phosphorylase from Yersinia pseudotuberculosis (YptUPh) was determined by X-ray diffraction at 1.7 Å resolution with high reliability (R work = 16.2, R free = 19.4%; r.m.s.d. of bond lengths and bond angles are 0.006 Å and 1.005°, respectively; DPI = 0.107 Å). The atoms of the amino acid residues of the functionally important secondary-structure elements—the loop L9 and the helix H8—of the enzyme YptUPh were located. The three-dimensional structure of the complex of YptUPh with modified trimethoprim—referred to as 53I—was determined by the computer simulation. It was shown that 53I is a pseudosubstrate of uridine phosphorylases, and its pyrimidine-2,4-diamine group is located in the phosphate-binding site of the enzyme YptUPh

Structure of a complex of uridine phosphorylase from Yersinia pseudotuberculosis with the modified bacteriostatic antibacterial drug determined by X-ray crystallography and computer analysis

Science.gov (United States)

Balaev, V. V.; Lashkov, A. A.; Gabdoulkhakov, A. G.; Seregina, T. A.; Dontsova, M. V.; Mikhailov, A. M.

2015-03-01

Pseudotuberculosis and bubonic plague are acute infectious diseases caused by the bacteria Yersinia pseudotuberculosis and Yersinia pestis. These diseases are treated, in particular, with trimethoprim and its modified analogues. However, uridine phosphorylases (pyrimidine nucleoside phosphorylases) that are present in bacterial cells neutralize the action of trimethoprim and its modified analogues on the cells. In order to reveal the character of the interaction of the drug with bacterial uridine phosphorylase, the atomic structure of the unligated molecule of uridine-specific pyrimidine nucleoside phosphorylase from Yersinia pseudotuberculosis ( YptUPh) was determined by X-ray diffraction at 1.7 Å resolution with high reliability ( R work = 16.2, R free = 19.4%; r.m.s.d. of bond lengths and bond angles are 0.006 Å and 1.005°, respectively; DPI = 0.107 Å). The atoms of the amino acid residues of the functionally important secondary-structure elements—the loop L9 and the helix H8—of the enzyme YptUPh were located. The three-dimensional structure of the complex of YptUPh with modified trimethoprim—referred to as 53I—was determined by the computer simulation. It was shown that 53I is a pseudosubstrate of uridine phosphorylases, and its pyrimidine-2,4-diamine group is located in the phosphate-binding site of the enzyme YptUPh.

Discrete symmetries and the complex structure of Calabi-Yau manifolds

International Nuclear Information System (INIS)

Ross, G.G.

1988-01-01

We show how the discrete symmetries, which may be present after Calabi-Yau compactification for specific choices of the complex structure, extend to the h 2,1 moduli - the scalar fields whose vacuum expectation values determine the complex structure. This allows us to determine much about the coupling of the moduli and hence the energetically favoured complex structure. The discrete symmetry transformation properties of the moduli are worked out in detail for a three-generation Calabi-Yau model and it is shown how minimization of the effective potential involving these fields selects the complex structure which leaves unbroken a set of discrete symmetries. The phenomenological implications of the symmetries are briefly discussed. (orig.)

Statistical and computer analysis for the solvent effect on the elctronis adsorption spectra of monoethanolamine complexes

International Nuclear Information System (INIS)

Masoud, M.S.; Motaweh, H.A.; Ali, A.E.

1999-01-01

Full text.the electronic absorption spectra of the octahedral complexes containing monoethanolamine were recorded in different solvents (dioxine, chlororm, ethanol, dimethylformamide, dimethylsulfoxide and water). The data analyzed based on multiple linear regression technique using the equation: ya (a is the regression intercept) are various empirical solvent polarytiparameters; constants are calculated using micro statistic program on pc computer. The solvent spectral data of the complexes are compared to that of nugot, the solvent assists the spectral data to be red shifts. In case of Mn (MEA) CL complex, numerous bands are appeared in presence of CHCI DMF and DMSO solvents probably due to the numerous oxidation states. The solvent parameters: E (solvent-solute hydrogen bond and dipolar interaction); (dipolar interaction related to the dielectric constant); M (solute permanent dipole-solvent induced ipole) and N (solute permanent dipole-solvent permanent dipole) are correlated with the structure of the complexes, in hydrogen bonding solvents (Band in case of complexes as the dielectric constant increases, blue shift occurs in due to conjugation with high stability, the data in DMF and DMSO solvents are nearly the same probably due to their similarity

Shapes of interacting RNA complexes

DEFF Research Database (Denmark)

Fu, Benjamin Mingming; Reidys, Christian

2014-01-01

Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....

Modeling the Structure and Complexity of Engineering Routine Design Problems

NARCIS (Netherlands)

Jauregui Becker, Juan Manuel; Wits, Wessel Willems; van Houten, Frederikus J.A.M.

2011-01-01

This paper proposes a model to structure routine design problems as well as a model of its design complexity. The idea is that having a proper model of the structure of such problems enables understanding its complexity, and likewise, a proper understanding of its complexity enables the development

Complex 3D Vortex Lattice Formation by Phase-Engineered Multiple Beam Interference

Directory of Open Access Journals (Sweden)

Jolly Xavier

2012-01-01

Full Text Available We present the computational results on the formation of diverse complex 3D vortex lattices by a designed superposition of multiple plane waves. Special combinations of multiples of three noncoplanar plane waves with a designed relative phase shift between one another are perturbed by a nonsingular beam to generate various complex 3D vortex lattice structures. The formation of complex gyrating lattice structures carrying designed vortices by means of relatively phase-engineered plane waves is also computationally investigated. The generated structures are configured with both periodic as well as transversely quasicrystallographic basis, while these whirling complex lattices possess a long-range order of designed symmetry in a given plane. Various computational analytical tools are used to verify the presence of engineered geometry of vortices in these complex 3D vortex lattices.

Evaluation of integration methods for hybrid simulation of complex structural systems through collapse

Science.gov (United States)

Del Carpio R., Maikol; Hashemi, M. Javad; Mosqueda, Gilberto

2017-10-01

This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

Crystal structure of the Msx-1 homeodomain/DNA complex.

Science.gov (United States)

Hovde, S; Abate-Shen, C; Geiger, J H

2001-10-09

The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

Metallacyclopentadienes: structural features and coordination in transition metal complexes

International Nuclear Information System (INIS)

Dolgushin, Fedor M; Yanovsky, Aleksandr I; Antipin, Mikhail Yu

2004-01-01

Results of structural studies of polynuclear transition metal complexes containing the metallacyclopentadiene fragment are overviewed. The structural features of the complexes in relation to the nature of the substituents in the organic moiety of the metallacycles, the nature of the transition metals and their ligand environment are analysed. The main structural characteristics corresponding to different modes of coordination of metallacyclopentadienes to one or two additional metal centres are revealed.

Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching

Science.gov (United States)

2013-01-01

REPORT Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The stable matching...Franceschetti 858-822-2284 3. DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - Jealousy Graphs: Structure and...market. Using this structure, we are able to provide a ner analysis of the complexity of a subclass of decentralized matching markets. Jealousy

Three-dimensional structure of the γ-secretase complex

International Nuclear Information System (INIS)

Ogura, Toshihiko; Mio, Kazuhiro; Hayashi, Ikuo; Miyashita, Hiroyuki; Fukuda, Rie; Kopan, Raphael; Kodama, Tatsuhiko; Hamakubo, Takao; Iwastubo, Takeshi; Tomita, Taisuke; Sato, Chikara

2006-01-01

γ-Secretase belongs to an atypical class of aspartic proteases that hydrolyzes peptide bonds within the transmembrane domain of substrates, including amyloid-β precursor protein and Notch. γ-Secretase is comprised of presenilin, nicastrin, APH-1, and PEN-2 which form a large multimeric membrane protein complex, the three-dimensional structure of which is unknown. To gain insight into the structure of this complex enzyme, we purified functional γ-secretase complex reconstituted in Sf9 cells and analyzed it using negative stain electron microscopy and 3D reconstruction techniques. Analysis of 2341 negatively stained particle images resulted in the three-dimensional representation of γ-secretase at a resolution of 48 A. The structure occupies a volume of 560 x 320 x 240 A and resembles a flat heart comprised of two oppositely faced, dimpled domains. A low density space containing multiple pores resides between the domains. Some of the dimples in the putative transmembrane region may house the catalytic site. The large dimensions are consistent with the observation that γ-secretase activity resides within a high molecular weight complex

New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

Science.gov (United States)

Tabti, Salima; Djedouani, Amel; Aggoun, Djouhra; Warad, Ismail; Rahmouni, Samra; Romdhane, Samir; Fouzi, Hosni

2018-03-01

The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

Structure of rhenium (5) complexes with petroleum organic sulfur compounds

International Nuclear Information System (INIS)

Akhmadieva, R.G.; Yusupova, N.A.; Numanov, N.U.; Basitova, S.M.

1985-01-01

Structure of Re(5) complexes with petroleum sulfides (L) of ReOCl 3 (L) 2 composition is studied by the UV- and IR-spectroscopy method in a short-wave and long-wave ranges. It is shown that Re(5) complex with L are of the form of flattened octahedron,where three Cl atoms and one L molecule are arranged in the plane around Re atom. The structure is analogous to structure of Re complexes with synthetic cyclic sulfides

Foundations of computer vision computational geometry, visual image structures and object shape detection

CERN Document Server

Peters, James F

2017-01-01

This book introduces the fundamentals of computer vision (CV), with a focus on extracting useful information from digital images and videos. Including a wealth of methods used in detecting and classifying image objects and their shapes, it is the first book to apply a trio of tools (computational geometry, topology and algorithms) in solving CV problems, shape tracking in image object recognition and detecting the repetition of shapes in single images and video frames. Computational geometry provides a visualization of topological structures such as neighborhoods of points embedded in images, while image topology supplies us with structures useful in the analysis and classification of image regions. Algorithms provide a practical, step-by-step means of viewing image structures. The implementations of CV methods in Matlab and Mathematica, classification of chapter problems with the symbols (easily solved) and (challenging) and its extensive glossary of key words, examples and connections with the fabric of C...

Data Structures in Classical and Quantum Computing

NARCIS (Netherlands)

M.J. Fillinger (Max)

2013-01-01

textabstractThis survey summarizes several results about quantum computing related to (mostly static) data structures. First, we describe classical data structures for the set membership and the predecessor search problems: Perfect Hash tables for set membership by Fredman, Koml\\'{o}s and

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

Science.gov (United States)

Rivas, Elena; Lang, Raymond; Eddy, Sean R

2012-02-01

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

CERN Document Server

2014-01-01

Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

Solar proton exposure of an ICRU sphere within a complex structure Part I: Combinatorial geometry.

Science.gov (United States)

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

2016-06-01

The 3DHZETRN code, with improved neutron and light ion (Z≤2) transport procedures, was recently developed and compared to Monte Carlo (MC) simulations using simplified spherical geometries. It was shown that 3DHZETRN agrees with the MC codes to the extent they agree with each other. In the present report, the 3DHZETRN code is extended to enable analysis in general combinatorial geometry. A more complex shielding structure with internal parts surrounding a tissue sphere is considered and compared against MC simulations. It is shown that even in the more complex geometry, 3DHZETRN agrees well with the MC codes and maintains a high degree of computational efficiency. Published by Elsevier Ltd.

Characterization of measurement errors using structure-from-motion and photogrammetry to measure marine habitat structural complexity.

Science.gov (United States)

Bryson, Mitch; Ferrari, Renata; Figueira, Will; Pizarro, Oscar; Madin, Josh; Williams, Stefan; Byrne, Maria

2017-08-01

Habitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure-from-motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time. This study evaluated the accuracy, precision, and bias in measurements of marine habitat structural complexity derived from structure-from-motion and photogrammetric measurements using repeated surveys of artificial reefs (with known structure) as well as natural coral reefs. We quantified measurement errors as a function of survey image coverage, actual surface rugosity, and the morphological community composition of the habitat-forming organisms (reef corals). Our results indicated that measurements could be biased by up to 7.5% of the total observed ranges of structural complexity based on the environmental conditions present during any particular survey. Positive relationships were found between measurement errors and actual complexity, and the strength of these relationships was increased when coral morphology and abundance were also used as predictors. The numerous advantages of structure-from-motion and photogrammetry techniques for quantifying and investigating marine habitats will mean that they are likely to replace traditional measurement techniques (e.g., chain-and-tape). To this end, our results have important implications for data collection and the interpretation of measurements when examining changes in habitat complexity using structure-from-motion and photogrammetry.

Chemistry and structure of technetium complexes

International Nuclear Information System (INIS)

Baldas, J.; Boas, J.F.; Bonnyman, J.; Williams, G.A.

1983-01-01

The structures of tris(2-aminobenzenethiolato) technetium(VI) and dichlorobis(diethyldithiocarbamato) thionitrosyltechnetium(V) have been determined by single crystal x-ray diffraction analysis. The preparation and chemistry of thiocyanato complexes of technetium have been investigated

The Intelligent Safety System: could it introduce complex computing into CANDU shutdown systems

International Nuclear Information System (INIS)

Hall, J.A.; Hinds, H.W.; Pensom, C.F.; Barker, C.J.; Jobse, A.H.

1984-07-01

The Intelligent Safety System is a computerized shutdown system being developed at the Chalk River Nuclear Laboratories (CRNL) for future CANDU nuclear reactors. It differs from current CANDU shutdown systems in both the algorithm used and the size and complexity of computers required to implement the concept. This paper provides an overview of the project, with emphasis on the computing aspects. Early in the project several needs leading to an introduction of computing complexity were identified, and a computing system that met these needs was conceived. The current work at CRNL centers on building a laboratory demonstration of the Intelligent Safety System, and evaluating the reliability and testability of the concept. Some fundamental problems must still be addressed for the Intelligent Safety System to be acceptable to a CANDU owner and to the regulatory authorities. These are also discussed along with a description of how the Intelligent Safety System might solve these problems

On The Computational Capabilities of Physical Systems. Part 2; Relationship With Conventional Computer Science

Science.gov (United States)

Wolpert, David H.; Koga, Dennis (Technical Monitor)

2000-01-01

In the first of this pair of papers, it was proven that there cannot be a physical computer to which one can properly pose any and all computational tasks concerning the physical universe. It was then further proven that no physical computer C can correctly carry out all computational tasks that can be posed to C. As a particular example, this result means that no physical computer that can, for any physical system external to that computer, take the specification of that external system's state as input and then correctly predict its future state before that future state actually occurs; one cannot build a physical computer that can be assured of correctly "processing information faster than the universe does". These results do not rely on systems that are infinite, and/or non-classical, and/or obey chaotic dynamics. They also hold even if one uses an infinitely fast, infinitely dense computer, with computational powers greater than that of a Turing Machine. This generality is a direct consequence of the fact that a novel definition of computation - "physical computation" - is needed to address the issues considered in these papers, which concern real physical computers. While this novel definition does not fit into the traditional Chomsky hierarchy, the mathematical structure and impossibility results associated with it have parallels in the mathematics of the Chomsky hierarchy. This second paper of the pair presents a preliminary exploration of some of this mathematical structure. Analogues of Chomskian results concerning universal Turing Machines and the Halting theorem are derived, as are results concerning the (im)possibility of certain kinds of error-correcting codes. In addition, an analogue of algorithmic information complexity, "prediction complexity", is elaborated. A task-independent bound is derived on how much the prediction complexity of a computational task can differ for two different reference universal physical computers used to solve that task

Cognitive engineering models: A prerequisite to the design of human-computer interaction in complex dynamic systems

Science.gov (United States)

Mitchell, Christine M.

1993-01-01

This chapter examines a class of human-computer interaction applications, specifically the design of human-computer interaction for the operators of complex systems. Such systems include space systems (e.g., manned systems such as the Shuttle or space station, and unmanned systems such as NASA scientific satellites), aviation systems (e.g., the flight deck of 'glass cockpit' airplanes or air traffic control) and industrial systems (e.g., power plants, telephone networks, and sophisticated, e.g., 'lights out,' manufacturing facilities). The main body of human-computer interaction (HCI) research complements but does not directly address the primary issues involved in human-computer interaction design for operators of complex systems. Interfaces to complex systems are somewhat special. The 'user' in such systems - i.e., the human operator responsible for safe and effective system operation - is highly skilled, someone who in human-machine systems engineering is sometimes characterized as 'well trained, well motivated'. The 'job' or task context is paramount and, thus, human-computer interaction is subordinate to human job interaction. The design of human interaction with complex systems, i.e., the design of human job interaction, is sometimes called cognitive engineering.

Integrative structure and functional anatomy of a nuclear pore complex

Science.gov (United States)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

Science.gov (United States)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Reduced-Complexity Direction of Arrival Estimation Using Real-Valued Computation with Arbitrary Array Configurations

Directory of Open Access Journals (Sweden)

Feng-Gang Yan

2018-01-01

Full Text Available A low-complexity algorithm is presented to dramatically reduce the complexity of the multiple signal classification (MUSIC algorithm for direction of arrival (DOA estimation, in which both tasks of eigenvalue decomposition (EVD and spectral search are implemented with efficient real-valued computations, leading to about 75% complexity reduction as compared to the standard MUSIC. Furthermore, the proposed technique has no dependence on array configurations and is hence suitable for arbitrary array geometries, which shows a significant implementation advantage over most state-of-the-art unitary estimators including unitary MUSIC (U-MUSIC. Numerical simulations over a wide range of scenarios are conducted to show the performance of the new technique, which demonstrates that with a significantly reduced computational complexity, the new approach is able to provide a close accuracy to the standard MUSIC.

Computing Mass Properties From AutoCAD

Science.gov (United States)

Jones, A.

1990-01-01

Mass properties of structures computed from data in drawings. AutoCAD to Mass Properties (ACTOMP) computer program developed to facilitate quick calculations of mass properties of structures containing many simple elements in such complex configurations as trusses or sheet-metal containers. Mathematically modeled in AutoCAD or compatible computer-aided design (CAD) system in minutes by use of three-dimensional elements. Written in Microsoft Quick-Basic (Version 2.0).

Complex-Dynamic Cosmology and Emergent World Structure

OpenAIRE

Kirilyuk, Andrei P.

2004-01-01

Universe structure emerges in the unreduced, complex-dynamic interaction process with the simplest initial configuration (two attracting homogeneous fields, quant-ph/9902015). The unreduced interaction analysis gives intrinsically creative cosmology, describing the real, explicitly emerging world structure with dynamic randomness on each scale. Without imposing any postulates or entities, we obtain physically real space, time, elementary particles with their detailed structure and intrinsic p...

Synthesis of Efficient Structures for Concurrent Computation.

Science.gov (United States)

1983-10-01

formal presentation of these techniques, called virtualisation and aggregation, can be found n [King-83$. 113.2 Census Functions Trees perform broadcast... Functions .. .. .. .. ... .... ... ... .... ... ... ....... 6 4 User-Assisted Aggregation .. .. .. .. ... ... ... .... ... .. .......... 6 5 Parallel...6. Simple Parallel Structure for Broadcasting .. .. .. .. .. . ... .. . .. . .... 4 Figure 7. Internal Structure of a Prefix Computation Network

Three-dimensional protein structure prediction: Methods and computational strategies.

Science.gov (United States)

Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C

2014-10-12

A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complexity and Dynamical Depth

Directory of Open Access Journals (Sweden)

Terrence Deacon

2014-07-01

Full Text Available We argue that a critical difference distinguishing machines from organisms and computers from brains is not complexity in a structural sense, but a difference in dynamical organization that is not well accounted for by current complexity measures. We propose a measure of the complexity of a system that is largely orthogonal to computational, information theoretic, or thermodynamic conceptions of structural complexity. What we call a system’s dynamical depth is a separate dimension of system complexity that measures the degree to which it exhibits discrete levels of nonlinear dynamical organization in which successive levels are distinguished by local entropy reduction and constraint generation. A system with greater dynamical depth than another consists of a greater number of such nested dynamical levels. Thus, a mechanical or linear thermodynamic system has less dynamical depth than an inorganic self-organized system, which has less dynamical depth than a living system. Including an assessment of dynamical depth can provide a more precise and systematic account of the fundamental difference between inorganic systems (low dynamical depth and living systems (high dynamical depth, irrespective of the number of their parts and the causal relations between them.

Detecting community structure using label propagation with consensus weight in complex network

International Nuclear Information System (INIS)

Liang Zong-Wen; Li Jian-Ping; Yang Fan; Petropulu Athina

2014-01-01

Community detection is a fundamental work to analyse the structural and functional properties of complex networks. The label propagation algorithm (LPA) is a near linear time algorithm to find a good community structure. Despite various subsequent advances, an important issue of this algorithm has not yet been properly addressed. Random update orders within the algorithm severely hamper the stability of the identified community structure. In this paper, we executed the basic label propagation algorithm on networks multiple times, to obtain a set of consensus partitions. Based on these consensus partitions, we created a consensus weighted graph. In this consensus weighted graph, the weight value of the edge was the proportion value that the number of node pairs allocated in the same cluster was divided by the total number of partitions. Then, we introduced consensus weight to indicate the direction of label propagation. In label update steps, by computing the mixing value of consensus weight and label frequency, a node adopted the label which has the maximum mixing value instead of the most frequent one. For extending to different networks, we introduced a proportion parameter to adjust the proportion of consensus weight and label frequency in computing mixing value. Finally, we proposed an approach named the label propagation algorithm with consensus weight (LPAcw), and the experimental results showed that the LPAcw could enhance considerably both the stability and the accuracy of community partitions. (interdisciplinary physics and related areas of science and technology)

A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

Science.gov (United States)

2010-01-01

Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Methods Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Results Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA.

Science.gov (United States)

D'Onofrio, David J; An, Gary

2010-01-21

The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological systems do not have an

A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

Directory of Open Access Journals (Sweden)

D'Onofrio David J

2010-01-01

Full Text Available Abstract Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Methods Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1 orthogonal uniqueness, (2 low level formatting, (3 high level formatting and (4 translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Results Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT during high level formatting of the computer hard drive and the subsequent loading of an operating

Mathematical modellings and computational methods for structural analysis of LMFBR's

International Nuclear Information System (INIS)

Liu, W.K.; Lam, D.

1983-01-01

In this paper, two aspects of nuclear reactor problems are discussed, modelling techniques and computational methods for large scale linear and nonlinear analyses of LMFBRs. For nonlinear fluid-structure interaction problem with large deformation, arbitrary Lagrangian-Eulerian description is applicable. For certain linear fluid-structure interaction problem, the structural response spectrum can be found via 'added mass' approach. In a sense, the fluid inertia is accounted by a mass matrix added to the structural mass. The fluid/structural modes of certain fluid-structure problem can be uncoupled to get the reduced added mass. The advantage of this approach is that it can account for the many repeated structures of nuclear reactor. In regard to nonlinear dynamic problem, the coupled nonlinear fluid-structure equations usually have to be solved by direct time integration. The computation can be very expensive and time consuming for nonlinear problems. Thus, it is desirable to optimize the accuracy and computation effort by using implicit-explicit mixed time integration method. (orig.)

On a computational method for modelling complex ecosystems by superposition procedure

International Nuclear Information System (INIS)

He Shanyu.

1986-12-01

In this paper, the Superposition Procedure is concisely described, and a computational method for modelling a complex ecosystem is proposed. With this method, the information contained in acceptable submodels and observed data can be utilized to maximal degree. (author). 1 ref

A design of a computer complex including vector processors

International Nuclear Information System (INIS)

Asai, Kiyoshi

1982-12-01

We, members of the Computing Center, Japan Atomic Energy Research Institute have been engaged for these six years in the research of adaptability of vector processing to large-scale nuclear codes. The research has been done in collaboration with researchers and engineers of JAERI and a computer manufacturer. In this research, forty large-scale nuclear codes were investigated from the viewpoint of vectorization. Among them, twenty-six codes were actually vectorized and executed. As the results of the investigation, it is now estimated that about seventy percents of nuclear codes and seventy percents of our total amount of CPU time of JAERI are highly vectorizable. Based on the data obtained by the investigation, (1)currently vectorizable CPU time, (2)necessary number of vector processors, (3)necessary manpower for vectorization of nuclear codes, (4)computing speed, memory size, number of parallel 1/0 paths, size and speed of 1/0 buffer of vector processor suitable for our applications, (5)necessary software and operational policy for use of vector processors are discussed, and finally (6)a computer complex including vector processors is presented in this report. (author)

Complex-plane strategy for computing rotating polytropic models - efficiency and accuracy of the complex first-order perturbation theory

International Nuclear Information System (INIS)

Geroyannis, V.S.

1988-01-01

In this paper, a numerical method is developed for determining the structure distortion of a polytropic star which rotates either uniformly or differentially. This method carries out the required numerical integrations in the complex plane. The method is implemented to compute indicative quantities, such as the critical perturbation parameter which represents an upper limit in the rotational behavior of the star. From such indicative results, it is inferred that this method achieves impressive improvement against other relevant methods; most important, it is comparable to some of the most elaborate and accurate techniques on the subject. It is also shown that the use of this method with Chandrasekhar's first-order perturbation theory yields an immediate drastic improvement of the results. Thus, there is no neeed - for most applications concerning rotating polytropic models - to proceed to the further use of the method with higher order techniques, unless the maximum accuracy of the method is required. 31 references

Computational Approaches to Nucleic Acid Origami.

Science.gov (United States)

Jabbari, Hosna; Aminpour, Maral; Montemagno, Carlo

2015-10-12

Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.

Generation of tooth-periodontium complex structures using high-odontogenic potential dental epithelium derived from mouse embryonic stem cells.

Science.gov (United States)

Zhang, Yancong; Li, Yongliang; Shi, Ruirui; Zhang, Siqi; Liu, Hao; Zheng, Yunfei; Li, Yan; Cai, Jinglei; Pei, Duanqing; Wei, Shicheng

2017-06-08

A number of studies have shown that tooth-like structures can be regenerated using induced pluripotent stem cells and mouse embryonic stem (mES) cells. However, few studies have reported the regeneration of tooth-periodontium complex structures, which are more suitable for clinical tooth transplantation. We established an optimized approach to induce high-odontogenic potential dental epithelium derived from mES cells by temporally controlling bone morphogenic protein 4 (BMP4) function and regenerated tooth-periodontium complex structures in vivo. First, immunofluorescence and quantitative reverse transcription-polymerase chain reaction were used to identify the watershed of skin and the oral ectoderm. LDN193189 was then used to inhibit the BMP4 receptor around the watershed, followed by the addition of exogenous BMP4 to promote BMP4 function. The generated dental epithelium was confirmed by western blot analysis and immunofluorescence. The generated epithelium was ultimately combined with embryonic day 14.5 mouse mesenchyme and transplanted into the renal capsules of nude mice. After 4 weeks, the tooth-periodontium complex structure was examined by micro-computed tomography (CT) and hematoxylin and eosin (H&E) staining. Our study found that the turning point of oral ectoderm differentiation occurred around day 3 after the embryoid body was transferred to a common culture plate. Ameloblastin-positive dental epithelial cells were detected following the temporal regulation of BMP4. Tooth-periodontium complex structures, which included teeth, a periodontal membrane, and alveolar bone, were formed when this epithelium was combined with mouse dental mesenchyme and transplanted into the renal capsules of nude mice. Micro-CT and H&E staining revealed that the generated tooth-periodontium complex structures shared a similar histological structure with normal mouse teeth. An optimized induction method was established to promote the differentiation of mES cells into dental

Uranium complexes with macrosyclic polyethers. Synthesis and structural chemical analysis

International Nuclear Information System (INIS)

Elbasyouny, A.

1983-01-01

This dissertation reports about studies on the chemical coordination behaviour of uranium of oxidation stages IV and VI with regard to twelve different macrocyclic ligands. For the preparation of the complexes, for every system a different method has been developed. The elementary analysis of the various complexes including the uranium had been done by X-ray fluorescence analysis, and the structural characterization proceeded via vibrational, uv-vis and emission spectroscopy as well as 1 H-NMR and 13 C-spin-lattice relaxation time studies. Conformational analysis of the polyethers used allowed the structural changes in the complexes to be observed. The structural analysis of the hydrous uranium VI crown ether complexes yielded information of characteristic features of these types of complexes. The first coordination sphere of the uranyl ion with covalently bonded anion remains unchanged. As to the water content, there is a certain range. Depending upon the solvent used, the complexes have two or four H 2 O molecules per formula unit. (orig./EF) [de

GAS PHASE STRUCTURE AND STABILITY OF COMPLEX FORMED BY H2O, NH3, H2S AND THEIR METHYL DERIVATIVES WITH THE CATION CO2+

Directory of Open Access Journals (Sweden)

Cahyorini Kusumawardani

2010-06-01

Full Text Available Ab initio molecular orbital calculations at the Hartree-Fock-Self Consistent Field (HF-SCF have been performed in order to determine the structure and gas phase energies of complex formed by the Lewis bases of H2O, NH3, H2S and their methyl derivatives with the cation Co2+. The relative basicities of the base studied depend on both the substituent. The gas-phase interaction energies computed by the SCF method including electron correlation Møller-Plesset 2 (MP2 dan Configuration Iteration (CI were comparable in accuracy. The binding energies computed by these two methods reach the targeted chemical accuracy.   Keywords: ab initio calculation, cobalt complex, structure stability

Collective network for computer structures

Science.gov (United States)

Blumrich, Matthias A [Ridgefield, CT; Coteus, Paul W [Yorktown Heights, NY; Chen, Dong [Croton On Hudson, NY; Gara, Alan [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Hoenicke, Dirk [Ossining, NY; Takken, Todd E [Brewster, NY; Steinmacher-Burow, Burkhard D [Wernau, DE; Vranas, Pavlos M [Bedford Hills, NY

2011-08-16

A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices ate included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network and class structures. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to needs of a processing algorithm.

Investigation of anticancer properties of caffeinated complexes via computational chemistry methods

Science.gov (United States)

Sayin, Koray; Üngördü, Ayhan

2018-03-01

Computational investigations were performed for 1,3,7-trimethylpurine-2,6-dione, 3,7-dimethylpurine-2,6-dione, their Ru(II) and Os(III) complexes. B3LYP/6-311 ++G(d,p)(LANL2DZ) level was used in numerical calculations. Geometric parameters, IR spectrum, 1H-, 13C and 15N NMR spectrum were examined in detail. Additionally, contour diagram of frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) maps, MEP contour and some quantum chemical descriptors were used in the determination of reactivity rankings and active sites. The electron density on the surface was similar to each other in studied complexes. Quantum chemical descriptors were investigated and the anticancer activity of complexes were more than cisplatin and their ligands. Additionally, molecular docking calculations were performed in water between related complexes and a protein (ID: 3WZE). The most interact complex was found as Os complex. The interaction energy was calculated as 342.9 kJ/mol.

Effects of Task Performance and Task Complexity on the Validity of Computational Models of Attention

NARCIS (Netherlands)

Koning, L. de; Maanen, P.P. van; Dongen, K. van

2008-01-01

Computational models of attention can be used as a component of decision support systems. For accurate support, a computational model of attention has to be valid and robust. The effects of task performance and task complexity on the validity of three different computational models of attention were

Reducing the Computational Complexity of Reconstruction in Compressed Sensing Nonuniform Sampling

DEFF Research Database (Denmark)

Grigoryan, Ruben; Jensen, Tobias Lindstrøm; Arildsen, Thomas

2013-01-01

sparse signals, but requires computationally expensive reconstruction algorithms. This can be an obstacle for real-time applications. The reduction of complexity is achieved by applying a multi-coset sampling procedure. This proposed method reduces the size of the dictionary matrix, the size...

Complexity and Intensionality in a Type-1 Framework for Computable Analysis

DEFF Research Database (Denmark)

Lambov, Branimir Zdravkov

2005-01-01

This paper describes a type-1 framework for computable analysis designed to facilitate efficient implementations and discusses properties that have not been well studied before for type-1 approaches: the introduction of complexity measures for type-1 representations of real functions, and ways...

Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies

KAUST Repository

Aboulhassan, A.

2017-07-04

The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state-of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.

Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies

KAUST Repository

Aboulhassan, A.; Sicat, R.; Baum, D.; Wodo, O.; Hadwiger, Markus

2017-01-01

The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state-of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.

Computational chemistry and metal-based radiopharmaceuticals

International Nuclear Information System (INIS)

Neves, M.; Fausto, R.

1998-01-01

Computer-assisted techniques have found extensive use in the design of organic pharmaceuticals but have not been widely applied on metal complexes, particularly on radiopharmaceuticals. Some examples of computer generated structures of complexes of In, Ga and Tc with N, S, O and P donor ligands are referred. Besides parameters directly related with molecular geometries, molecular properties of the predicted structures, as ionic charges or dipole moments, are considered to be related with biodistribution studies. The structure of a series of oxo neutral Tc-biguanide complexes are predicted by molecular mechanics calculations, and their interactions with water molecules or peptide chains correlated with experimental data of partition coefficients and percentage of human protein binding. The results stress the interest of using molecular modelling to predict molecular properties of metal-based radiopharmaceuticals, which can be successfully correlated with results of in vitro studies. (author)

Computer simulations of dendrimer-polyelectrolyte complexes.

Science.gov (United States)

Pandav, Gunja; Ganesan, Venkat

2014-08-28

We carry out a systematic analysis of static properties of the clusters formed by complexation between charged dendrimers and linear polyelectrolyte (LPE) chains in a dilute solution under good solvent conditions. We use single chain in mean-field simulations and analyze the structure of the clusters through radial distribution functions of the dendrimer, cluster size, and charge distributions. The effects of LPE length, charge ratio between LPE and dendrimer, the influence of salt concentration, and the dendrimer generation number are examined. Systems with short LPEs showed a reduced propensity for aggregation with dendrimers, leading to formation of smaller clusters. In contrast, larger dendrimers and longer LPEs lead to larger clusters with significant bridging. Increasing salt concentration was seen to reduce aggregation between dendrimers as a result of screening of electrostatic interactions. Generally, maximum complexation was observed in systems with an equal amount of net dendrimer and LPE charges, whereas either excess LPE or dendrimer concentrations resulted in reduced clustering between dendrimers.

Impact of familiarity on information complexity in human-computer interfaces

Directory of Open Access Journals (Sweden)

Bakaev Maxim

2016-01-01

Full Text Available A quantitative measure of information complexity remains very much desirable in HCI field, since it may aid in optimization of user interfaces, especially in human-computer systems for controlling complex objects. Our paper is dedicated to exploration of subjective (subject-depended aspect of the complexity, conceptualized as information familiarity. Although research of familiarity in human cognition and behaviour is done in several fields, the accepted models in HCI, such as Human Processor or Hick-Hyman’s law do not generally consider this issue. In our experimental study the subjects performed search and selection of digits and letters, whose familiarity was conceptualized as frequency of occurrence in numbers and texts. The analysis showed significant effect of information familiarity on selection time and throughput in regression models, although the R2 values were somehow low. Still, we hope that our results might aid in quantification of information complexity and its further application for optimizing interaction in human-machine systems.

Complex Data Modeling and Computationally Intensive Statistical Methods

CERN Document Server

Mantovan, Pietro

2010-01-01

The last years have seen the advent and development of many devices able to record and store an always increasing amount of complex and high dimensional data; 3D images generated by medical scanners or satellite remote sensing, DNA microarrays, real time financial data, system control datasets. The analysis of this data poses new challenging problems and requires the development of novel statistical models and computational methods, fueling many fascinating and fast growing research areas of modern statistics. The book offers a wide variety of statistical methods and is addressed to statistici

Computational Architecture of the Granular Layer of Cerebellum-Like Structures.

Science.gov (United States)

Bratby, Peter; Sneyd, James; Montgomery, John

2017-02-01

In the adaptive filter model of the cerebellum, the granular layer performs a recoding which expands incoming mossy fibre signals into a temporally diverse set of basis signals. The underlying neural mechanism is not well understood, although various mechanisms have been proposed, including delay lines, spectral timing and echo state networks. Here, we develop a computational simulation based on a network of leaky integrator neurons, and an adaptive filter performance measure, which allows candidate mechanisms to be compared. We demonstrate that increasing the circuit complexity improves adaptive filter performance, and relate this to evolutionary innovations in the cerebellum and cerebellum-like structures in sharks and electric fish. We show how recurrence enables an increase in basis signal duration, which suggest a possible explanation for the explosion in granule cell numbers in the mammalian cerebellum.

Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream

Directory of Open Access Journals (Sweden)

Elyashberg Mikhail

2009-03-01

Full Text Available Abstract Background This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE. The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. Results The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of "nonstandard" length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. Conclusion The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist's dream of "fully automated structure elucidation" there is

Quantum chemical investigation of levofloxacin-boron complexes: A computational approach

Science.gov (United States)

Sayin, Koray; Karakaş, Duran

2018-04-01

Quantum chemical calculations are performed over some boron complexes with levofloxacin. Boron complex with fluorine atoms are optimized at three different methods (HF, B3LYP and M062X) with 6-31 + G(d) basis set. The best level is determined as M062X/6-31 + G(d) by comparison of experimental and calculated results of complex (1). The other complexes are optimized by using the best level. Structural properties, IR and NMR spectrum are examined in detail. Biological activities of mentioned complexes are investigated by some quantum chemical descriptors and molecular docking analyses. As a result, biological activities of complex (2) and (4) are close to each other and higher than those of other complexes. Additionally, NLO properties of mentioned complexes are investigated by some quantum chemical parameters. It is found that complex (3) is the best candidate for NLO applications.

Information visualization for the Structural Complexity Management Approach

OpenAIRE

Maurer, Maik;Braun, Thomas;Lindemann, Udo

2017-01-01

The handling of complexity poses an important challenge and a success factor for product design. A considerable percentage of complexity results from dependencies between system elements – as adaptations to single system elements can cause far-reaching consequences. The Structural Complexity Management (SCM) approach provides a five-step procedure that supports users in the identification, acquisition, analysis and optimization of system dependencies. The approach covers the handling of multi...

Communication complexity and information complexity

Science.gov (United States)

Pankratov, Denis

Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information

Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires

Directory of Open Access Journals (Sweden)

Enkelejda Miho

2018-02-01

Full Text Available The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV. Adaptive immune receptor repertoire sequencing (AIRR-seq has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i diversity, (ii clustering and network, (iii phylogenetic, and (iv machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.

Structure of a stacked anthraquinone–DNA complex

Science.gov (United States)

De Luchi, Daniela; Usón, Isabel; Wright, Glenford; Gouyette, Catherine; Subirana, Juan A.

2010-01-01

The crystal structure of the telomeric sequence d(UBrAGG) interacting with an anthraquinone derivative has been solved by MAD. In all previously studied complexes of intercalating drugs, the drug is usually sandwiched between two DNA base pairs. Instead, the present structure looks like a crystal of stacked anthraquinone molecules in which isolated base pairs are intercalated. Unusual base pairs are present in the structure, such as G·G and A·UBr reverse Watson–Crick base pairs. PMID:20823516

Automated analysis and design of complex structures

International Nuclear Information System (INIS)

Wilson, E.L.

1977-01-01

This paper discusses the following: 1. The relationship of analysis to design. 2. New methods of analysis. 3. Improved finite elements. 4. Effect of minicomputer on structural analysis methods. 5. The use of system of microprocessors for nonlinear structural analysis. 6. The role of interacting graphics systems in future analysis and design. The discussion focusses on the impact of new inexpensive computer hardware on design and analysis methods. (Auth.)

Computer-aided visualization of database structural relationships

International Nuclear Information System (INIS)

Cahn, D.F.

1980-04-01

Interactive computer graphic displays can be extremely useful in augmenting understandability of data structures. In complexly interrelated domains such as bibliographic thesauri and energy information systems, node and link displays represent one such tool. This paper presents examples of data structure representations found useful in these domains and discusses some of their generalizable components. 2 figures

Soil structure characterized using computed tomographic images

Science.gov (United States)

Zhanqi Cheng; Stephen H. Anderson; Clark J. Gantzer; J. W. Van Sambeek

2003-01-01

Fractal analysis of soil structure is a relatively new method for quantifying the effects of management systems on soil properties and quality. The objective of this work was to explore several methods of studying images to describe and quantify structure of soils under forest management. This research uses computed tomography and a topological method called Multiple...

Giga-voxel computational morphogenesis for structural design

Science.gov (United States)

Aage, Niels; Andreassen, Erik; Lazarov, Boyan S.; Sigmund, Ole

2017-10-01

In the design of industrial products ranging from hearing aids to automobiles and aeroplanes, material is distributed so as to maximize the performance and minimize the cost. Historically, human intuition and insight have driven the evolution of mechanical design, recently assisted by computer-aided design approaches. The computer-aided approach known as topology optimization enables unrestricted design freedom and shows great promise with regard to weight savings, but its applicability has so far been limited to the design of single components or simple structures, owing to the resolution limits of current optimization methods. Here we report a computational morphogenesis tool, implemented on a supercomputer, that produces designs with giga-voxel resolution—more than two orders of magnitude higher than previously reported. Such resolution provides insights into the optimal distribution of material within a structure that were hitherto unachievable owing to the challenges of scaling up existing modelling and optimization frameworks. As an example, we apply the tool to the design of the internal structure of a full-scale aeroplane wing. The optimized full-wing design has unprecedented structural detail at length scales ranging from tens of metres to millimetres and, intriguingly, shows remarkable similarity to naturally occurring bone structures in, for example, bird beaks. We estimate that our optimized design corresponds to a reduction in mass of 2-5 per cent compared to currently used aeroplane wing designs, which translates into a reduction in fuel consumption of about 40-200 tonnes per year per aeroplane. Our morphogenesis process is generally applicable, not only to mechanical design, but also to flow systems, antennas, nano-optics and micro-systems.

Development of a Computer Application to Simulate Porous Structures

Directory of Open Access Journals (Sweden)

S.C. Reis

2002-09-01

Full Text Available Geometric modeling is an important tool to evaluate structural parameters as well as to follow the application of stereological relationships. The obtention, visualization and analysis of volumetric images of the structure of materials, using computational geometric modeling, facilitates the determination of structural parameters of difficult experimental access, such as topological and morphological parameters. In this work, we developed a geometrical model implemented by computer software that simulates random pore structures. The number of nodes, number of branches (connections between nodes and the number of isolated parts, are obtained. Also, the connectivity (C is obtained from this application. Using a list of elements, nodes and branches, generated by the software, in AutoCAD® command line format, the obtained structure can be viewed and analyzed.

Computer methods for transient fluid-structure analysis of nuclear reactors

International Nuclear Information System (INIS)

Belytschko, T.; Liu, W.K.

1985-01-01

Fluid-structure interaction problems in nuclear engineering are categorized according to the dominant physical phenomena and the appropriate computational methods. Linear fluid models that are considered include acoustic fluids, incompressible fluids undergoing small disturbances, and small amplitude sloshing. Methods available in general-purpose codes for these linear fluid problems are described. For nonlinear fluid problems, the major features of alternative computational treatments are reviewed; some special-purpose and multipurpose computer codes applicable to these problems are then described. For illustration, some examples of nuclear reactor problems that entail coupled fluid-structure analysis are described along with computational results

Composition of complex numbers: Delineating the computational role of the left anterior temporal lobe.

Science.gov (United States)

Blanco-Elorrieta, Esti; Pylkkänen, Liina

2016-01-01

What is the neurobiological basis of our ability to create complex messages with language? Results from multiple methodologies have converged on a set of brain regions as relevant for this general process, but the computational details of these areas remain to be characterized. The left anterior temporal lobe (LATL) has been a consistent node within this network, with results suggesting that although it rather systematically shows increased activation for semantically complex structured stimuli, this effect does not extend to number phrases such as 'three books.' In the present work we used magnetoencephalography to investigate whether numbers in general are an invalid input to the combinatory operations housed in the LATL or whether the lack of LATL engagement for stimuli such as 'three books' is due to the quantificational nature of such phrases. As a relevant test case, we employed complex number terms such as 'twenty-three', where one number term is not a quantifier of the other but rather, the two terms form a type of complex concept. In a number naming paradigm, participants viewed rows of numbers and depending on task instruction, named them as complex number terms ('twenty-three'), numerical quantifications ('two threes'), adjectival modifications ('blue threes') or non-combinatory lists (e.g., 'two, three'). While quantificational phrases failed to engage the LATL as compared to non-combinatory controls, both complex number terms and adjectival modifications elicited a reliable activity increase in the LATL. Our results show that while the LATL does not participate in the enumeration of tokens within a set, exemplified by the quantificational phrases, it does support conceptual combination, including the composition of complex number concepts. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Quasi-brittle material behavior under cyclic loading: from virtual testing to structural computation

International Nuclear Information System (INIS)

Vassaux, Maxime

2015-01-01

Macroscopic constitutive laws are developed not only because they allow for large-scale computations but also because refine dissipative mechanisms observed at lower scales. Within the framework of this study, the development of such models is carried out in the context of seismic loading, that is to say reverse cyclic loading, applied to the quasi-brittle materials and more precisely, concrete-like materials. Nowadays, robust and predictive macroscopic constitutive laws are still rare because of the complexity of cracking related phenomena. Among the challenges to face, the material parameters identification is far from being the easiest due to the lack of experimental data. Indeed, the difficulties to carry out cyclic tests on concrete-like materials are numerous. To overcome these difficulties, a virtual testing approach based on a refine model is proposed in this study in order to feed continuum models with the missing material parameters. Adopting a microscopic point of view, a representative volume element is seen as a structure. The microscopic model has been developed with the aim to require a minimal number of material parameters which only need basic mechanical tests to be identified. From an existing lattice model developed to deal with monotonic loading, several enhancements have been realized in order to extend its range of applicability, making it capable of dealing with complex multi-axial cyclic loadings. The microscopic model has been validated as a virtual testing machine that is able to help the identification procedure of continuous constitutive laws. This identification approach has been applied on a new constitutive law developed within the framework of isotropic continuum damage mechanics accounting for cyclic related effects. In particular, the concept of regularized unilateral effect has been introduced to describe the progressive crack closure. The macroscopic model has been calibrated with the help from the aforementioned virtual testing

Curvilinear immersed boundary method for simulating fluid structure interaction with complex 3D rigid bodies

Science.gov (United States)

Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2008-08-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable even when strong coupling FSI is employed. For such cases, however, combining the strong coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI

LT^2C^2: A language of thought with Turing-computable Kolmogorov complexity

Directory of Open Access Journals (Sweden)

Santiago Figueira

2013-03-01

Full Text Available In this paper, we present a theoretical effort to connect the theory of program size to psychology by implementing a concrete language of thought with Turing-computable Kolmogorov complexity (LT^2C^2 satisfying the following requirements: 1 to be simple enough so that the complexity of any given finite binary sequence can be computed, 2 to be based on tangible operations of human reasoning (printing, repeating,. . . , 3 to be sufficiently powerful to generate all possible sequences but not too powerful as to identify regularities which would be invisible to humans. We first formalize LT^2C^2, giving its syntax and semantics, and defining an adequate notion of program size. Our setting leads to a Kolmogorov complexity function relative to LT^2C^2 which is computable in polynomial time, and it also induces a prediction algorithm in the spirit of Solomonoff’s inductive inference theory. We then prove the efficacy of this language by investigating regularities in strings produced by participants attempting to generate random strings. Participants had a profound understanding of randomness and hence avoided typical misconceptions such as exaggerating the number of alternations. We reasoned that remaining regularities would express the algorithmic nature of human thoughts, revealed in the form of specific patterns. Kolmogorov complexity relative to LT^2C^2 passed three expected tests examined here: 1 human sequences were less complex than control PRNG sequences, 2 human sequences were not stationary showing decreasing values of complexity resulting from fatigue 3 each individual showed traces of algorithmic stability since fitting of partial data was more effective to predict subsequent data than average fits. This work extends on previous efforts to combine notions of Kolmogorov complexity theory and algorithmic information theory to psychology, by explicitly proposing a language which may describe the patterns of human thoughts.Received: 12

On the Computational Capabilities of Physical Systems. Part 1; The Impossibility of Infallible Computation

Science.gov (United States)

Wolpert, David H.; Koga, Dennis (Technical Monitor)

2000-01-01

In this first of two papers, strong limits on the accuracy of physical computation are established. First it is proven that there cannot be a physical computer C to which one can pose any and all computational tasks concerning the physical universe. Next it is proven that no physical computer C can correctly carry out any computational task in the subset of such tasks that can be posed to C. This result holds whether the computational tasks concern a system that is physically isolated from C, or instead concern a system that is coupled to C. As a particular example, this result means that there cannot be a physical computer that can, for any physical system external to that computer, take the specification of that external system's state as input and then correctly predict its future state before that future state actually occurs; one cannot build a physical computer that can be assured of correctly 'processing information faster than the universe does'. The results also mean that there cannot exist an infallible, general-purpose observation apparatus, and that there cannot be an infallible, general-purpose control apparatus. These results do not rely on systems that are infinite, and/or non-classical, and/or obey chaotic dynamics. They also hold even if one uses an infinitely fast, infinitely dense computer, with computational powers greater than that of a Turing Machine. This generality is a direct consequence of the fact that a novel definition of computation - a definition of 'physical computation' - is needed to address the issues considered in these papers. While this definition does not fit into the traditional Chomsky hierarchy, the mathematical structure and impossibility results associated with it have parallels in the mathematics of the Chomsky hierarchy. The second in this pair of papers presents a preliminary exploration of some of this mathematical structure, including in particular that of prediction complexity, which is a 'physical computation

Synthesis of computational structures for analog signal processing

CERN Document Server

Popa, Cosmin Radu

2011-01-01

Presents the most important classes of computational structures for analog signal processing, including differential or multiplier structures, squaring or square-rooting circuits, exponential or Euclidean distance structures and active resistor circuitsIntroduces the original concept of the multifunctional circuit, an active structure that is able to implement, starting from the same circuit core, a multitude of continuous mathematical functionsCovers mathematical analysis, design and implementation of a multitude of function generator structures

Analyzing the Implicit Computational Complexity of object-oriented programs

OpenAIRE

Marion , Jean-Yves; Péchoux , Romain

2008-01-01

International audience; A sup-interpretation is a tool which provides upper bounds on the size of the values computed by the function symbols of a program. Sup-interpretations have shown their interest to deal with the complexity of first order functional programs. This paper is an attempt to adapt the framework of sup-interpretations to a fragment of object-oriented programs, including loop and while constructs and methods with side effects. We give a criterion, called brotherly criterion, w...

Designing complex systems - a structured activity

NARCIS (Netherlands)

van der Veer, Gerrit C.; van Vliet, Johannes C.; Lenting, Bert; Olson, Gary M.; Schuon, Sue

1995-01-01

This paper concerns the development of complex systems from the point of view of design as a structure of activities, related both to the clients and the users. Several modeling approaches will be adopted for different aspects of design, and several views on design will be integrated. The proposed

GAM-HEAT -- a computer code to compute heat transfer in complex enclosures

International Nuclear Information System (INIS)

Cooper, R.E.; Taylor, J.R.; Kielpinski, A.L.; Steimke, J.L.

1991-02-01

The GAM-HEAT code was developed for heat transfer analyses associated with postulated Double Ended Guillotine Break Loss Of Coolant Accidents (DEGB LOCA) resulting in a drained reactor vessel. In these analyses the gamma radiation resulting from fission product decay constitutes the primary source of energy as a function of time. This energy is deposited into the various reactor components and is re- radiated as thermal energy. The code accounts for all radiant heat exchanges within and leaving the reactor enclosure. The SRS reactors constitute complex radiant exchange enclosures since there are many assemblies of various types within the primary enclosure and most of the assemblies themselves constitute enclosures. GAM-HEAT accounts for this complexity by processing externally generated view factors and connectivity matrices, and also accounts for convective, conductive, and advective heat exchanges. The code is applicable for many situations involving heat exchange between surfaces within a radiatively passive medium. The GAM-HEAT code has been exercised extensively for computing transient temperatures in SRS reactors with specific charges and control components. Results from these computations have been used to establish the need for and to evaluate hardware modifications designed to mitigate results of postulated accident scenarios, and to assist in the specification of safe reactor operating power limits. The code utilizes temperature dependence on material properties. The efficiency of the code has been enhanced by the use of an iterative equation solver. Verification of the code to date consists of comparisons with parallel efforts at Los Alamos National Laboratory and with similar efforts at Westinghouse Science and Technology Center in Pittsburgh, PA, and benchmarked using problems with known analytical or iterated solutions. All comparisons and tests yield results that indicate the GAM-HEAT code performs as intended

The structural robustness of multiprocessor computing system

Directory of Open Access Journals (Sweden)

N. Andronaty

1996-03-01

Full Text Available The model of the multiprocessor computing system on the base of transputers which permits to resolve the question of valuation of a structural robustness (viability, survivability is described.

The evolution of cerebellum structure correlates with nest complexity.

Science.gov (United States)

Hall, Zachary J; Street, Sally E; Healy, Susan D

2013-01-01

Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulative skills. Here, we tested this hypothesis by investigating the relationship between cerebellar foliation and species-typical nest structure in birds. Increasing complexity of nest structure is a measure of a bird's ability to manipulate nesting material into the required shape. Consistent with our hypothesis, avian cerebellar foliation increases as the complexity of the nest built increases, setting the scene for the exploration of nest building at the neural level.

Computer-Aided Design of RNA Origami Structures.

Science.gov (United States)

Sparvath, Steffen L; Geary, Cody W; Andersen, Ebbe S

2017-01-01

RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

On the structure and spin states of Fe(III)-EDDHA complexes.

Science.gov (United States)

Gómez-Gallego, Mar; Fernández, Israel; Pellico, Daniel; Gutiérrez, Angel; Sierra, Miguel A; Lucena, Juan J

2006-07-10

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.

Computation: A New Open Access Journal of Computational Chemistry, Computational Biology and Computational Engineering

Directory of Open Access Journals (Sweden)

Karlheinz Schwarz

2013-09-01

Full Text Available Computation (ISSN 2079-3197; http://www.mdpi.com/journal/computation is an international scientific open access journal focusing on fundamental work in the field of computational science and engineering. Computational science has become essential in many research areas by contributing to solving complex problems in fundamental science all the way to engineering. The very broad range of application domains suggests structuring this journal into three sections, which are briefly characterized below. In each section a further focusing will be provided by occasionally organizing special issues on topics of high interests, collecting papers on fundamental work in the field. More applied papers should be submitted to their corresponding specialist journals. To help us achieve our goal with this journal, we have an excellent editorial board to advise us on the exciting current and future trends in computation from methodology to application. We very much look forward to hearing all about the research going on across the world. [...

Three-dimensional structure of a pre-catalytic human spliceosomal complex B.

Science.gov (United States)

Boehringer, Daniel; Makarov, Evgeny M; Sander, Bjoern; Makarova, Olga V; Kastner, Berthold; Lührmann, Reinhard; Stark, Holger

2004-05-01

Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have immunoaffinity-purified human spliceosomes (designated B Delta U1) at a stage after U4/U6.U5 tri-snRNP integration but before activation, and have determined the three-dimensional structure of B Delta U1 by single-particle electron cryomicroscopy at a resolution of approximately 40 A. The overall size of the complex is about 370 x 270 x 170 A. The three-dimensional structure features a roughly triangular body linked to a head domain in variable orientations. The body is very similar in size and shape to the isolated U4/U6.U5 tri-snRNP. This provides initial insight into the structural organization of complex B.

Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.

Science.gov (United States)

Pan, Yuliang; Wang, Zixiang; Zhan, Weihua; Deng, Lei

2018-05-01

Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein-RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result. The PrabHot webserver is freely available at http://denglab.org/PrabHot/. leideng@csu.edu.cn. Supplementary data are available at Bioinformatics online.

Computational applications of DNA structural scales

DEFF Research Database (Denmark)

Baldi, P.; Chauvin, Y.; Brunak, Søren

1998-01-01

that these scales provide an alternative or complementary compact representation of DNA sequences. As an example, we construct a strand-invariant representation of DNA sequences. The scales can also be used to analyze and discover new DNA structural patterns, especially in combination with hidden Markov models......Studies several different physical scales associated with the structural features of DNA sequences from a computational standpoint, including dinucleotide scales, such as base stacking energy and propeller twist, and trinucleotide scales, such as bendability and nucleosome positioning. We show...

High-performance computing for structural mechanics and earthquake/tsunami engineering

CERN Document Server

Hori, Muneo; Ohsaki, Makoto

2016-01-01

Huge earthquakes and tsunamis have caused serious damage to important structures such as civil infrastructure elements, buildings and power plants around the globe.  To quantitatively evaluate such damage processes and to design effective prevention and mitigation measures, the latest high-performance computational mechanics technologies, which include telascale to petascale computers, can offer powerful tools. The phenomena covered in this book include seismic wave propagation in the crust and soil, seismic response of infrastructure elements such as tunnels considering soil-structure interactions, seismic response of high-rise buildings, seismic response of nuclear power plants, tsunami run-up over coastal towns and tsunami inundation considering fluid-structure interactions. The book provides all necessary information for addressing these phenomena, ranging from the fundamentals of high-performance computing for finite element methods, key algorithms of accurate dynamic structural analysis, fluid flows ...

Communication Complexity A treasure house of lower bounds

Indian Academy of Sciences (India)

Prahladh Harsha TIFR

Applications. Data structures, VLSI design, time-space tradeoffs, circuit complexity, streaming, auctions, combinatorial optimization . . . Randomized Communication Complexity of INTER: Ω(n). ▷ There is no parallelizable monotone circuit that computes a matching in a given graph ...

Theory of computational complexity

CERN Document Server

Du, Ding-Zhu

2011-01-01

DING-ZHU DU, PhD, is a professor in the Department of Computer Science at the University of Minnesota. KER-I KO, PhD, is a professor in the Department of Computer Science at the State University of New York at Stony Brook.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

Science.gov (United States)

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Using the calculational simulating complexes when making the computer process control systems for NPP

International Nuclear Information System (INIS)

Zimakov, V.N.; Chernykh, V.P.

1998-01-01

The problems on creating calculational-simulating (CSC) and their application by developing the program and program-technical means for computer-aided process control systems at NPP are considered. The abo- ve complex is based on the all-mode real time mathematical model, functioning at a special complex of computerized means

PSPP: a protein structure prediction pipeline for computing clusters.

Directory of Open Access Journals (Sweden)

Michael S Lee

2009-07-01

Full Text Available Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.The pipeline consists of a Perl core that integrates more than 20 individual software packages and databases, most of which are freely available from other research laboratories. The query protein sequences are first divided into domains either by domain boundary recognition or Bayesian statistics. The structures of the individual domains are then predicted using template-based modeling or ab initio modeling. The predicted models are scored with a statistical potential and an all-atom force field. The top-scoring ab initio models are annotated by structural comparison against the Structural Classification of Proteins (SCOP fold database. Furthermore, secondary structure, solvent accessibility, transmembrane helices, and structural disorder are predicted. The results are generated in text, tab-delimited, and hypertext markup language (HTML formats. So far, the pipeline has been used to study viral and bacterial proteomes.The standalone pipeline that we introduce here, unlike protein structure prediction Web servers, allows users to devote their own computing assets to process a potentially unlimited number of queries as well as perform

Computational complexity of symbolic dynamics at the onset of chaos

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Lakdawala, Porus

1996-05-01

In a variety of studies of dynamical systems, the edge of order and chaos has been singled out as a region of complexity. It was suggested by Wolfram, on the basis of qualitative behavior of cellular automata, that the computational basis for modeling this region is the universal Turing machine. In this paper, following a suggestion of Crutchfield, we try to show that the Turing machine model may often be too powerful as a computational model to describe the boundary of order and chaos. In particular we study the region of the first accumulation of period doubling in unimodal and bimodal maps of the interval, from the point of view of language theory. We show that in relation to the ``extended'' Chomsky hierarchy, the relevant computational model in the unimodal case is the nested stack automaton or the related indexed languages, while the bimodal case is modeled by the linear bounded automaton or the related context-sensitive languages.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

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Chen Chun

2008-03-01

Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

Vulnerability of coral reef fisheries to a loss of structural complexity.

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Rogers, Alice; Blanchard, Julia L; Mumby, Peter J

2014-05-05

Coral reefs face a diverse array of threats, from eutrophication and overfishing to climate change. As live corals are lost and their skeletons eroded, the structural complexity of reefs declines. This may have important consequences for the survival and growth of reef fish because complex habitats mediate predator-prey interactions [1, 2] and influence competition [3-5] through the provision of prey refugia. A positive correlation exists between structural complexity and reef fish abundance and diversity in both temperate and tropical ecosystems [6-10]. However, it is not clear how the diversity of available refugia interacts with individual predator-prey relationships to explain emergent properties at the community scale. Furthermore, we do not yet have the ability to predict how habitat loss might affect the productivity of whole reef communities and the fisheries they support. Using data from an unfished reserve in The Bahamas, we find that structural complexity is associated not only with increased fish biomass and abundance, but also with nonlinearities in the size spectra of fish, implying disproportionately high abundances of certain size classes. By developing a size spectrum food web model that links the vulnerability of prey to predation with the structural complexity of a reef, we show that these nonlinearities can be explained by size-structured prey refugia that reduce mortality rates and alter growth rates in different parts of the size spectrum. Fitting the model with data from a structurally complex habitat, we predict that a loss of complexity could cause more than a 3-fold reduction in fishery productivity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structural insights into SUN-KASH complexes across the nuclear envelope

Institute of Scientific and Technical Information of China (English)

Wenjia Wang; Zhaocai Zhou; Zhubing Shi; Shi Jiao; Cuicui Chen; Huizhen Wang; Guoguang Liu; Qiang Wang; Yun Zhao; Mark I Greene

2012-01-01

Linker of the nucleoskeleton and the cytoskeleton (LINC) complexes are composed of SUN and KASH domaincontaining proteins and bridge the inner and outer membranes of the nuclear envelope.LINC complexes play critical roles in nuclear positioning,cell polarization and cellular stiffness.Previously,we reported the homotrimeric structure of human SUN2.We have now determined the crystal structure of the human SUN2-KASH complex.In the complex structure,the SUN domain homotrimer binds to three independent "hook"-like KASH peptides.The overall conformation of the SUN domain in the complex closely resembles the SUN domain in its apo state.A major conformational change involves the AA'-loop of KASH-bound SUN domain,which rearranges to form a mini β-sheet that interacts with the KASH peptide.The PPPT motif of the KASH domain fits tightly into a hydrophobic pocket on the homotrimeric interface of the SUN domain,which we termed the BI-pocket.Moreover,two adjacent protomers of the SUN domain homotrimer sandwich the KASH domain by hydrophobic interaction and hydrogen bonding.Mutations of these binding sites disrupt or reduce the association between the SUN and KASH domains in vitro.In addition,transfection of wild-type,but not mutant,SUN2 promotes cell migration in Ovcar-3 cells.These results provide a structural model of the LINC complex,which is essential for additional study of the physical and functional coupling between the cytoplasm and the nucleoplasm.

Survey of large protein complexes D. vulgaris reveals great structural diversity

Energy Technology Data Exchange (ETDEWEB)

Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

2009-08-15

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

Science.gov (United States)

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Recent developments of the NESSUS probabilistic structural analysis computer program

Science.gov (United States)

Millwater, H.; Wu, Y.-T.; Torng, T.; Thacker, B.; Riha, D.; Leung, C. P.

1992-01-01

The NESSUS probabilistic structural analysis computer program combines state-of-the-art probabilistic algorithms with general purpose structural analysis methods to compute the probabilistic response and the reliability of engineering structures. Uncertainty in loading, material properties, geometry, boundary conditions and initial conditions can be simulated. The structural analysis methods include nonlinear finite element and boundary element methods. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. The scope of the code has recently been expanded to include probabilistic life and fatigue prediction of structures in terms of component and system reliability and risk analysis of structures considering cost of failure. The code is currently being extended to structural reliability considering progressive crack propagation. Several examples are presented to demonstrate the new capabilities.

A user's manual of Tools for Error Estimation of Complex Number Matrix Computation (Ver.1.0)

International Nuclear Information System (INIS)

Ichihara, Kiyoshi.

1997-03-01

'Tools for Error Estimation of Complex Number Matrix Computation' is a subroutine library which aids the users in obtaining the error ranges of the complex number linear system's solutions or the Hermitian matrices' eigen values. This library contains routines for both sequential computers and parallel computers. The subroutines for linear system error estimation calulate norms of residual vectors, matrices's condition numbers, error bounds of solutions and so on. The error estimation subroutines for Hermitian matrix eigen values' derive the error ranges of the eigen values according to the Korn-Kato's formula. This user's manual contains a brief mathematical background of error analysis on linear algebra and usage of the subroutines. (author)

Physiological Dynamics in Demyelinating Diseases: Unraveling Complex Relationships through Computer Modeling

Directory of Open Access Journals (Sweden)

Jay S. Coggan

2015-09-01

Full Text Available Despite intense research, few treatments are available for most neurological disorders. Demyelinating diseases are no exception. This is perhaps not surprising considering the multifactorial nature of these diseases, which involve complex interactions between immune system cells, glia and neurons. In the case of multiple sclerosis, for example, there is no unanimity among researchers about the cause or even which system or cell type could be ground zero. This situation precludes the development and strategic application of mechanism-based therapies. We will discuss how computational modeling applied to questions at different biological levels can help link together disparate observations and decipher complex mechanisms whose solutions are not amenable to simple reductionism. By making testable predictions and revealing critical gaps in existing knowledge, such models can help direct research and will provide a rigorous framework in which to integrate new data as they are collected. Nowadays, there is no shortage of data; the challenge is to make sense of it all. In that respect, computational modeling is an invaluable tool that could, ultimately, transform how we understand, diagnose, and treat demyelinating diseases.

NMR study of structure of lanthanide complexes in solution

International Nuclear Information System (INIS)

Choppin, G.R.

1976-01-01

The diagnostic value PMR studies of diamagnetic lanthanide complexes to define the nature of the species in the lanthanide-pyruvate system is discussed. The use of NMR spectra of both diamagnetic and paramagnetic lanthanide complexes to obtain detailed structural information is reviewed

Structural aspects of inotropic bipyridine binding. Crystal structure determination to 1.9 A of the human serum transthyretin-milrinone complex.

Science.gov (United States)

Wojtczak, A; Luft, J R; Cody, V

1993-03-25

The crystal structure of human transthyretin (TTR) complexed with milrinone (2-methyl-5-cyano-3,4'-bipyridin-6(1H)-one), a positive inotropic cardiac agent, has been refined to R = 17.4% for 8-1.9-A resolution data. This report provides the first detailed description of protein interactions for an inotropic bipyridine agent which is an effective thyroid hormone binding competitor to transthyretin. Milrinone is bound along the 2-fold axis in the binding site with its substituted pyridone ring located deep within the channel of the two identical binding domains of the TTR tetramer. In this orientation the 5-cyano group occupies the same site as the 3'-iodine in the TTR complex with 3,3'-diiodothyronine (Wojtczak, A., Luft, J., and Cody, V. (1992) J. Biol. Chem. 267, 353-357), which is 3.5 A deeper in the channel than thyroxine (Blake, C. C. F., and Oately, S. J., (1977) Nature 268, 115-120). These structural results confirm computer modeling studies of milrinone structural homology with thyroxine and its TTR binding interactions and explain the effectiveness of milrinone competition for thyroxine binding to TTR. To understand the weaker binding affinity of the parent inotropic drug, amrinone (5-amino-3,4'-bipyridin-6(1H)-one), modeling studies of its TTR binding were carried out which indicate that the 5-amino group cannot participate in strong interactions with TTR and the lack of the 2-methyl further weakens amrinone binding.

DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Wallace, Susan S.

2008-02-21

The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

Science.gov (United States)

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Recent Developments in Complex Analysis and Computer Algebra

CERN Document Server

Kajiwara, Joji; Xu, Yongzhi

1999-01-01

This volume consists of papers presented in the special sessions on "Complex and Numerical Analysis", "Value Distribution Theory and Complex Domains", and "Use of Symbolic Computation in Mathematics Education" of the ISAAC'97 Congress held at the University of Delaware, during June 2-7, 1997. The ISAAC Congress coincided with a U.S.-Japan Seminar also held at the University of Delaware. The latter was supported by the National Science Foundation through Grant INT-9603029 and the Japan Society for the Promotion of Science through Grant MTCS-134. It was natural that the participants of both meetings should interact and consequently several persons attending the Congress also presented papers in the Seminar. The success of the ISAAC Congress and the U.S.-Japan Seminar has led to the ISAAC'99 Congress being held in Fukuoka, Japan during August 1999. Many of the same participants will return to this Seminar. Indeed, it appears that the spirit of the U.S.-Japan Seminar will be continued every second year as part of...

Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

Science.gov (United States)

Xu, Qifang; Malecka, Kimberly L.; Fink, Lauren; Jordan, E. Joseph; Duffy, Erin; Kolander, Samuel; Peterson, Jeffrey; Dunbrack, Roland L.

2016-01-01

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an “autophosphorylation complex.” We developed and applied a structural bioinformatics method to identify all such autophosphorylation kinase complexes in X-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which 5 complexes had not previously been described in the publications describing the crystal structures. These 5 consist of tyrosine residues in the N-terminal juxtamembrane regions of colony stimulating factor 1 receptor (CSF1R, Tyr561) and EPH receptor A2 (EPHA2, Tyr594), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr394) and insulin-like growth factor 1 receptor (IGF1R, Tyr1166), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser142). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro447 to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets. PMID:26628682

Computer aided drug design

Science.gov (United States)

Jain, A.

2017-08-01

Computer based method can help in discovery of leads and can potentially eliminate chemical synthesis and screening of many irrelevant compounds, and in this way, it save time as well as cost. Molecular modeling systems are powerful tools for building, visualizing, analyzing and storing models of complex molecular structure that can help to interpretate structure activity relationship. The use of various techniques of molecular mechanics and dynamics and software in Computer aided drug design along with statistics analysis is powerful tool for the medicinal chemistry to synthesis therapeutic and effective drugs with minimum side effect.

Wing-Body Aeroelasticity Using Finite-Difference Fluid/Finite-Element Structural Equations on Parallel Computers

Science.gov (United States)

Byun, Chansup; Guruswamy, Guru P.; Kutler, Paul (Technical Monitor)

1994-01-01

In recent years significant advances have been made for parallel computers in both hardware and software. Now parallel computers have become viable tools in computational mechanics. Many application codes developed on conventional computers have been modified to benefit from parallel computers. Significant speedups in some areas have been achieved by parallel computations. For single-discipline use of both fluid dynamics and structural dynamics, computations have been made on wing-body configurations using parallel computers. However, only a limited amount of work has been completed in combining these two disciplines for multidisciplinary applications. The prime reason is the increased level of complication associated with a multidisciplinary approach. In this work, procedures to compute aeroelasticity on parallel computers using direct coupling of fluid and structural equations will be investigated for wing-body configurations. The parallel computer selected for computations is an Intel iPSC/860 computer which is a distributed-memory, multiple-instruction, multiple data (MIMD) computer with 128 processors. In this study, the computational efficiency issues of parallel integration of both fluid and structural equations will be investigated in detail. The fluid and structural domains will be modeled using finite-difference and finite-element approaches, respectively. Results from the parallel computer will be compared with those from the conventional computers using a single processor. This study will provide an efficient computational tool for the aeroelastic analysis of wing-body structures on MIMD type parallel computers.

Solving complex and disordered surface structures with electron diffraction

International Nuclear Information System (INIS)

Van Hove, M.A.

1987-10-01

The past of surface structure determination with low-energy electron diffraction (LEED) will be briefly reviewed, setting the stage for a discussion of recent and future developments. The aim of these developments is to solve complex and disordered surface structures. Some efficient solutions to the theoretical and experimental problems will be presented. Since the theoretical problems dominate, the emphasis will be on theoretical approaches to the calculation of the multiple scattering of electrons through complex and disordered surfaces. 49 refs., 13 figs., 1 tab

Structure-function relationship in complex brain networks expressed by hierarchical synchronization

International Nuclear Information System (INIS)

Zhou Changsong; Zemanova, Lucia; Zamora-Lopez, Gorka; Hilgetag, Claus C; Kurths, Juergen

2007-01-01

The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks

Structure-function relationship in complex brain networks expressed by hierarchical synchronization

Energy Technology Data Exchange (ETDEWEB)

Zhou Changsong [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Zemanova, Lucia [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Zamora-Lopez, Gorka [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Hilgetag, Claus C [Jacobs University Bremen, Campus Ring 6, Rm 116, D-28759 Bremen (Germany); Kurths, Juergen [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany)

2007-06-15

The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks.

EXAFS Phase Retrieval Solution Tracking for Complex Multi-Component System: Synthesized Topological Inverse Computation

International Nuclear Information System (INIS)

Lee, Jay Min; Yang, Dong-Seok; Bunker, Grant B

2013-01-01

Using the FEFF kernel A(k,r), we describe the inverse computation from χ(k)-data to g(r)-solution in terms of a singularity regularization method based on complete Bayesian statistics process. In this work, we topologically decompose the system-matched invariant projection operators into two distinct types, (A + AA + A) and (AA + AA + ), and achieved Synthesized Topological Inversion Computation (STIC), by employing a 12-operator-closed-loop emulator of the symplectic transformation. This leads to a numerically self-consistent solution as the optimal near-singular regularization parameters are sought, dramatically suppressing instability problems connected with finite precision arithmetic in ill-posed systems. By statistically correlating a pair of measured data, it was feasible to compute an optimal EXAFS phase retrieval solution expressed in terms of the complex-valued χ(k), and this approach was successfully used to determine the optimal g(r) for a complex multi-component system.

Multi-frequency complex network from time series for uncovering oil-water flow structure.

Science.gov (United States)

Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

2015-02-04

Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

Pentacoordinated organoaluminum complexes: A computational insight

KAUST Repository

Milione, Stefano

2012-12-24

The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

Pentacoordinated organoaluminum complexes: A computational insight

KAUST Repository

Milione, Stefano; Milano, Giuseppe; Cavallo, Luigi

2012-01-01

The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

Toward Design Guidelines for Stream Restoration Structures: Measuring and Modeling Unsteady Turbulent Flows in Natural Streams with Complex Hydraulic Structures

Science.gov (United States)

Lightbody, A.; Sotiropoulos, F.; Kang, S.; Diplas, P.

2009-12-01

Despite their widespread application to prevent lateral river migration, stabilize banks, and promote aquatic habitat, shallow transverse flow training structures such as rock vanes and stream barbs lack quantitative design guidelines. Due to the lack of fundamental knowledge about the interaction of the flow field with the sediment bed, existing engineering standards are typically based on various subjective criteria or on cross-sectionally-averaged shear stresses rather than local values. Here, we examine the performance and stability of in-stream structures within a field-scale single-threaded sand-bed meandering stream channel in the newly developed Outdoor StreamLab (OSL) at the St. Anthony Falls Laboratory (SAFL). Before and after the installation of a rock vane along the outer bank of the middle meander bend, high-resolution topography data were obtained for the entire 50-m-long reach at 1-cm spatial scale in the horizontal and sub-millimeter spatial scale in the vertical. In addition, detailed measurements of flow and turbulence were obtained using acoustic Doppler velocimetry at twelve cross-sections focused on the vicinity of the structure. Measurements were repeated at a range of extreme events, including in-bank flows with an approximate flow rate of 44 L/s (1.4 cfs) and bankfull floods with an approximate flow rate of 280 L/s (10 cfs). Under both flow rates, the structure reduced near-bank shear stresses and resulted in both a deeper thalweg and near-bank aggradation. The resulting comprehensive dataset has been used to validate a large eddy simulation carried out by SAFL’s computational fluid dynamics model, the Virtual StreamLab (VSL). This versatile computational framework is able to efficiently simulate 3D unsteady turbulent flows in natural streams with complex in-stream structures and as a result holds promise for the development of much-needed quantitative design guidelines.

Distinguishing humans from computers in the game of go: A complex network approach

Science.gov (United States)

Coquidé, C.; Georgeot, B.; Giraud, O.

2017-08-01

We compare complex networks built from the game of go and obtained from databases of human-played games with those obtained from computer-played games. Our investigations show that statistical features of the human-based networks and the computer-based networks differ, and that these differences can be statistically significant on a relatively small number of games using specific estimators. We show that the deterministic or stochastic nature of the computer algorithm playing the game can also be distinguished from these quantities. This can be seen as a tool to implement a Turing-like test for go simulators.

Electronic structure and driving forces in β-cyclodextrin: Diclofenac inclusion complexes

International Nuclear Information System (INIS)

Bogdan, Diana; Morari, C.

2007-01-01

We investigate the geometry and electronic structure for complexes of β-cyclodextrin with diclofenac using DFT calculations. The effect of solvent is explicitly taken into account. This investigation allows us to draw meaningful conclusions upon the stability of the complex and the nature of the driving forces leading to the complexation process. In particular we emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries

Structure identification and adaptive synchronization of uncertain general complex dynamical networks

International Nuclear Information System (INIS)

Xu Yuhua; Zhou Wuneng; Fang Jian'an; Lu Hongqian

2009-01-01

This Letter proposes an approach to identify the topological structure and unknown parameters for uncertain general complex networks simultaneously. By designing effective adaptive controllers, we achieve synchronization between two complex networks. The unknown network topological structure and system parameters of uncertain general complex dynamical networks are identified simultaneously in the process of synchronization. Several useful criteria for synchronization are given. Finally, an illustrative example is presented to demonstrate the application of the theoretical results.

Structure identification and adaptive synchronization of uncertain general complex dynamical networks

Energy Technology Data Exchange (ETDEWEB)

Xu Yuhua, E-mail: yuhuaxu2004@163.co [College of Information Science and Technology, Donghua University, Shanghai 201620 (China) and Department of Maths, Yunyang Teacher' s College, Hubei 442000 (China); Zhou Wuneng, E-mail: wnzhou@163.co [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Fang Jian' an [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Lu Hongqian [Shandong Institute of Light Industry, Shandong Jinan 250353 (China)

2009-12-28

This Letter proposes an approach to identify the topological structure and unknown parameters for uncertain general complex networks simultaneously. By designing effective adaptive controllers, we achieve synchronization between two complex networks. The unknown network topological structure and system parameters of uncertain general complex dynamical networks are identified simultaneously in the process of synchronization. Several useful criteria for synchronization are given. Finally, an illustrative example is presented to demonstrate the application of the theoretical results.

Local likelihood estimation of complex tail dependence structures in high dimensions, applied to US precipitation extremes

KAUST Repository

Camilo, Daniela Castro

2017-10-02

In order to model the complex non-stationary dependence structure of precipitation extremes over the entire contiguous U.S., we propose a flexible local approach based on factor copula models. Our sub-asymptotic spatial modeling framework yields non-trivial tail dependence structures, with a weakening dependence strength as events become more extreme, a feature commonly observed with precipitation data but not accounted for in classical asymptotic extreme-value models. To estimate the local extremal behavior, we fit the proposed model in small regional neighborhoods to high threshold exceedances, under the assumption of local stationarity. This allows us to gain in flexibility, while making inference for such a large and complex dataset feasible. Adopting a local censored likelihood approach, inference is made on a fine spatial grid, and local estimation is performed taking advantage of distributed computing resources and of the embarrassingly parallel nature of this estimation procedure. The local model is efficiently fitted at all grid points, and uncertainty is measured using a block bootstrap procedure. An extensive simulation study shows that our approach is able to adequately capture complex, non-stationary dependencies, while our study of U.S. winter precipitation data reveals interesting differences in local tail structures over space, which has important implications on regional risk assessment of extreme precipitation events. A comparison between past and current data suggests that extremes in certain areas might be slightly wider in extent nowadays than during the first half of the twentieth century.

Local likelihood estimation of complex tail dependence structures in high dimensions, applied to US precipitation extremes

KAUST Repository

Camilo, Daniela Castro; Huser, Raphaë l

2017-01-01

In order to model the complex non-stationary dependence structure of precipitation extremes over the entire contiguous U.S., we propose a flexible local approach based on factor copula models. Our sub-asymptotic spatial modeling framework yields non-trivial tail dependence structures, with a weakening dependence strength as events become more extreme, a feature commonly observed with precipitation data but not accounted for in classical asymptotic extreme-value models. To estimate the local extremal behavior, we fit the proposed model in small regional neighborhoods to high threshold exceedances, under the assumption of local stationarity. This allows us to gain in flexibility, while making inference for such a large and complex dataset feasible. Adopting a local censored likelihood approach, inference is made on a fine spatial grid, and local estimation is performed taking advantage of distributed computing resources and of the embarrassingly parallel nature of this estimation procedure. The local model is efficiently fitted at all grid points, and uncertainty is measured using a block bootstrap procedure. An extensive simulation study shows that our approach is able to adequately capture complex, non-stationary dependencies, while our study of U.S. winter precipitation data reveals interesting differences in local tail structures over space, which has important implications on regional risk assessment of extreme precipitation events. A comparison between past and current data suggests that extremes in certain areas might be slightly wider in extent nowadays than during the first half of the twentieth century.

Nanofluidic structures with complex three-dimensional surfaces

International Nuclear Information System (INIS)

Stavis, Samuel M; Gaitan, Michael; Strychalski, Elizabeth A

2009-01-01

Nanofluidic devices have typically explored a design space of patterns limited by a single nanoscale structure depth. A method is presented here for fabricating nanofluidic structures with complex three-dimensional (3D) surfaces, utilizing a single layer of grayscale photolithography and standard integrated circuit manufacturing tools. This method is applied to construct nanofluidic devices with numerous (30) structure depths controlled from ∼10 to ∼620 nm with an average standard deviation of 1 cm. A prototype 3D nanofluidic device is demonstrated that implements size exclusion of rigid nanoparticles and variable nanoscale confinement and deformation of biomolecules.

Computational mesh generation for vascular structures with deformable surfaces

International Nuclear Information System (INIS)

Putter, S. de; Laffargue, F.; Breeuwer, M.; Vosse, F.N. van de; Gerritsen, F.A.; Philips Medical Systems, Best

2006-01-01

Computational blood flow and vessel wall mechanics simulations for vascular structures are becoming an important research tool for patient-specific surgical planning and intervention. An important step in the modelling process for patient-specific simulations is the creation of the computational mesh based on the segmented geometry. Most known solutions either require a large amount of manual processing or lead to a substantial difference between the segmented object and the actual computational domain. We have developed a chain of algorithms that lead to a closely related implementation of image segmentation with deformable models and 3D mesh generation. The resulting processing chain is very robust and leads both to an accurate geometrical representation of the vascular structure as well as high quality computational meshes. The chain of algorithms has been tested on a wide variety of shapes. A benchmark comparison of our mesh generation application with five other available meshing applications clearly indicates that the new approach outperforms the existing methods in the majority of cases. (orig.)

Local pulmonary structure classification for computer-aided nodule detection

Science.gov (United States)

Bahlmann, Claus; Li, Xianlin; Okada, Kazunori

2006-03-01

We propose a new method of classifying the local structure types, such as nodules, vessels, and junctions, in thoracic CT scans. This classification is important in the context of computer aided detection (CAD) of lung nodules. The proposed method can be used as a post-process component of any lung CAD system. In such a scenario, the classification results provide an effective means of removing false positives caused by vessels and junctions thus improving overall performance. As main advantage, the proposed solution transforms the complex problem of classifying various 3D topological structures into much simpler 2D data clustering problem, to which more generic and flexible solutions are available in literature, and which is better suited for visualization. Given a nodule candidate, first, our solution robustly fits an anisotropic Gaussian to the data. The resulting Gaussian center and spread parameters are used to affine-normalize the data domain so as to warp the fitted anisotropic ellipsoid into a fixed-size isotropic sphere. We propose an automatic method to extract a 3D spherical manifold, containing the appropriate bounding surface of the target structure. Scale selection is performed by a data driven entropy minimization approach. The manifold is analyzed for high intensity clusters, corresponding to protruding structures. Techniques involve EMclustering with automatic mode number estimation, directional statistics, and hierarchical clustering with a modified Bhattacharyya distance. The estimated number of high intensity clusters explicitly determines the type of pulmonary structures: nodule (0), attached nodule (1), vessel (2), junction (>3). We show accurate classification results for selected examples in thoracic CT scans. This local procedure is more flexible and efficient than current state of the art and will help to improve the accuracy of general lung CAD systems.

Development of an Evaluation Method for the Design Complexity of Computer-Based Displays

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyoung Ju; Lee, Seung Woo; Kang, Hyun Gook; Seong, Poong Hyun [KAIST, Daejeon (Korea, Republic of); Park, Jin Kyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2011-10-15

The importance of the design of human machine interfaces (HMIs) for human performance and the safety of process industries has long been continuously recognized for many decades. Especially, in the case of nuclear power plants (NPPs), HMIs have significant implications for the safety of the NPPs because poor HMIs can impair the decision making ability of human operators. In order to support and increase the decision making ability of human operators, advanced HMIs based on the up-to-date computer technology are provided. Human operators in advanced main control room (MCR) acquire information through video display units (VDUs) and large display panel (LDP), which is required for the operation of NPPs. These computer-based displays contain a huge amount of information and present it with a variety of formats compared to those of a conventional MCR. For example, these displays contain more display elements such as abbreviations, labels, icons, symbols, coding, etc. As computer-based displays contain more information, the complexity of advanced displays becomes greater due to less distinctiveness of each display element. A greater understanding is emerging about the effectiveness of designs of computer-based displays, including how distinctively display elements should be designed. This study covers the early phase in the development of an evaluation method for the design complexity of computer-based displays. To this end, a series of existing studies were reviewed to suggest an appropriate concept that is serviceable to unravel this problem

DNA complexes with Ni nanoparticles: structural and functional properties

Energy Technology Data Exchange (ETDEWEB)

Tatarinova, Olga N.; Smirnov, Igor P. [Research Institute for Physico-Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation (Russian Federation); Safenkova, Irina V. [A.N. Bach Institute of Biochemistry (Russian Federation); Varizhuk, Anna M.; Pozmogova, Galina E., E-mail: pozmge@gmail.com [Research Institute for Physico-Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation (Russian Federation)

2012-10-15

Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid-nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

DNA complexes with Ni nanoparticles: structural and functional properties

International Nuclear Information System (INIS)

Tatarinova, Olga N.; Smirnov, Igor P.; Safenkova, Irina V.; Varizhuk, Anna M.; Pozmogova, Galina E.

2012-01-01

Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid–nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

Wave propagation in complex structures with LEGO

NARCIS (Netherlands)

Lancellotti, V.; Hon, de B.P.; Tijhuis, A.G.

2012-01-01

We present the extension of the linear embedding via Green's operators (LEGO) scheme to problems that involve elementary sources localized inside complex structures made of different dielectric media with inclusions. We show how this new feature allows solving problems of wave propagation within,

Computational Investigation on the Spectroscopic Properties of Thiophene Based Europium β-Diketonate Complexes.

Science.gov (United States)

Greco, Claudio; Moro, Giorgio; Bertini, Luca; Biczysko, Malgorzata; Barone, Vincenzo; Cosentino, Ugo

2014-02-11

The adiabatic transition energies from the lowest triplet states of four Europium tris β-diketonate/phenantroline complexes have been determined in vacuo and in dicholomethane solution by the ΔSCF approach at the density functional theory level, using the PBE1PBE and the CAM-B3LYP hybrid functionals. The calculated adiabatic transition energies have been compared with the experimental 0-0 transitions of each complex determined from phosphorescence spectra of the corresponding Gd(3+) complexes and followed by direct comparison between simulated and experimental spectra line shapes. For compound 1, the Eu(TTA)3Phen system, triplet states other than the lowest one and conformational isomers other than the one present in the crystallographic structure have been considered. In the crystallographic structure, this compound presents three quasi-degenerate low energy triplet states, differing for the TTA ligand where the two unpaired electrons are localized and showing close adiabatic transition energies. For compound 1, the lowest triplet states of the four investigated conformational isomers show similar characteristics and close adiabatic transition energies. On the basis of these results, an investigation of compounds 2-4 (Eu(Br-TTA)3Phen, Eu(DTDK)3Phen, and Eu(MeT-TTA)3) has been performed by considering only the isomer present in the crystallographic structure and only the lowest triplet state of each compound. For compounds 1-3, the energies of the lowest triplet states calculated by both functionals in solution including zero-point energy corrections well reproduce the experimental trends as well as the values of the adiabatic transition energies: CAM-B3LYP, the best performing functional, provides energies of the lowest triplet state with deviations from experiments lower than 1200 cm(-1). Also, the calculated vibrationally resolved phosphorescence spectra and UV-vis absorptions well reproduce the main features of their experimental counterparts. Significant

Reaction-diffusion controlled growth of complex structures

Science.gov (United States)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes.

Science.gov (United States)

Kim, H; Lipscomb, W N

1990-06-12

O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity (Ki = 3 pM). Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis [Hanson, J. E., Kaplan, A. P., & Bartlett, P. A. (1989) Biochemistry 28, 6294-6305]. In the present study, the structure of the complex of this phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 A. The complex crystallizes in the space group P2(1)2(1)2(1) with cell dimensions a = 61.9 A, b = 67.2 A, and c = 76.2 A. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 A yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 A on the electrophilic (Arg-127) side and 3.1 A on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attacked by Zn-hydroxyl (or Zn-water). An unexpected feature of the bound inhibitor, the cis carbamoyl ester bond at the benzyloxycarbonyl linkage to alanine, allows the benzyloxycarbonyl phenyl ring of the inhibitor to interact favorably with Tyr-198. This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.

Efficient physical embedding of topologically complex information processing networks in brains and computer circuits.

Directory of Open Access Journals (Sweden)

Danielle S Bassett

2010-04-01

Full Text Available Nervous systems are information processing networks that evolved by natural selection, whereas very large scale integrated (VLSI computer circuits have evolved by commercially driven technology development. Here we follow historic intuition that all physical information processing systems will share key organizational properties, such as modularity, that generally confer adaptivity of function. It has long been observed that modular VLSI circuits demonstrate an isometric scaling relationship between the number of processing elements and the number of connections, known as Rent's rule, which is related to the dimensionality of the circuit's interconnect topology and its logical capacity. We show that human brain structural networks, and the nervous system of the nematode C. elegans, also obey Rent's rule, and exhibit some degree of hierarchical modularity. We further show that the estimated Rent exponent of human brain networks, derived from MRI data, can explain the allometric scaling relations between gray and white matter volumes across a wide range of mammalian species, again suggesting that these principles of nervous system design are highly conserved. For each of these fractal modular networks, the dimensionality of the interconnect topology was greater than the 2 or 3 Euclidean dimensions of the space in which it was embedded. This relatively high complexity entailed extra cost in physical wiring: although all networks were economically or cost-efficiently wired they did not strictly minimize wiring costs. Artificial and biological information processing systems both may evolve to optimize a trade-off between physical cost and topological complexity, resulting in the emergence of homologous principles of economical, fractal and modular design across many different kinds of nervous and computational networks.

The Similar Structures and Control Problems of Complex Systems

Institute of Scientific and Technical Information of China (English)

无

2002-01-01

In this paper, the naturally evolving complex systems, such as biotic and social ones, are considered. Focusing on their structures, a feature is noteworthy, i.e., the similarity in structures. The relations between the functions and behaviors of these systems and their similar structures will be studied. Owing to the management of social systems and the course of evolution of biotic systems may be regarded as control processes, the researches will be within the scope of control problems. Moreover, since it is difficult to model for biotic and social systems, it will start with the control problems of complex systems, possessing similar structures, in engineering.The obtained results show that for either linear or nonlinear systems and for a lot of control problemssimilar structures lead to a series of simplifications. In general, the original system may be decomposed into reduced amount of subsystems with lower dimensions and simpler structures. By virtue of such subsystems, the control problems of original system can be solved more simply.At last, it turns round to observe the biotic and social systems and some analyses are given.

Electronic structure and driving forces in {beta}-cyclodextrin: Diclofenac inclusion complexes

Energy Technology Data Exchange (ETDEWEB)

Bogdan, Diana [National Institute for Research and Development of Isotopic and Molecular Technologies, Donath street 71-103, 400293 Cluj-Napoca (Romania); Morari, C. [National Institute for Research and Development of Isotopic and Molecular Technologies, Donath street 71-103, 400293 Cluj-Napoca (Romania)]. E-mail: cristim@s3.itim-cj.ro

2007-07-02

We investigate the geometry and electronic structure for complexes of {beta}-cyclodextrin with diclofenac using DFT calculations. The effect of solvent is explicitly taken into account. This investigation allows us to draw meaningful conclusions upon the stability of the complex and the nature of the driving forces leading to the complexation process. In particular we emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries.

Computation of 3D form factors in complex environments

International Nuclear Information System (INIS)

Coulon, N.

1989-01-01

The calculation of radiant interchange among opaque surfaces in a complex environment poses the general problem of determining the visible and hidden parts of the environment. In many thermal engineering applications, surfaces are separated by radiatively non-participating media and may be idealized as diffuse emitters and reflectors. Consenquently the net radiant energy fluxes are intimately related to purely geometrical quantities called form factors, that take into account hidden parts: the problem is reduced to the form factor evaluation. This paper presents the method developed for the computation of 3D form factors in the finite-element module of the system TRIO, which is a general computer code for thermal and fluid flow analysis. The method is derived from an algorithm devised for synthetic image generation. A comparison is performed with the standard contour integration method also implemented and suited to convex geometries. Several illustrative examples of finite-element thermal calculations in radiating enclosures are given

Towards electromechanical computation: An alternative approach to realize complex logic circuits

KAUST Repository

Hafiz, Md Abdullah Al; Kosuru, Lakshmoji; Younis, Mohammad I.

2016-01-01

Electromechanical computing based on micro/nano resonators has recently attracted significant attention. However, full implementation of this technology has been hindered by the difficulty in realizing complex logic circuits. We report here an alternative approach to realize complex logic circuits based on multiple MEMS resonators. As case studies, we report the construction of a single-bit binary comparator, a single-bit 4-to-2 encoder, and parallel XOR/XNOR and AND/NOT logic gates. Toward this, several microresonators are electrically connected and their resonance frequencies are tuned through an electrothermal modulation scheme. The microresonators operating in the linear regime do not require large excitation forces, and work at room temperature and at modest air pressure. This study demonstrates that by reconfiguring the same basic building block, tunable resonator, several essential complex logic functions can be achieved.

Towards electromechanical computation: An alternative approach to realize complex logic circuits

KAUST Repository

Hafiz, M. A. A.

2016-08-18

Electromechanical computing based on micro/nano resonators has recently attracted significant attention. However, full implementation of this technology has been hindered by the difficulty in realizing complex logic circuits. We report here an alternative approach to realize complex logic circuits based on multiple MEMS resonators. As case studies, we report the construction of a single-bit binary comparator, a single-bit 4-to-2 encoder, and parallel XOR/XNOR and AND/NOT logic gates. Toward this, several microresonators are electrically connected and their resonance frequencies are tuned through an electrothermal modulation scheme. The microresonators operating in the linear regime do not require large excitation forces, and work at room temperature and at modest air pressure. This study demonstrates that by reconfiguring the same basic building block, tunable resonator, several essential complex logic functions can be achieved.

On dependence of stability of lanthanum complexes with aminopolycarboxylic acids on the complex structure

International Nuclear Information System (INIS)

Poluehktov, N.S.; Meshkova, S.B.; Danilkovich, M.M.; Topilova, Z.M.

1985-01-01

Regularities in changes of stability constants of lanthanum complexes with aminopolycarboxylic acids (APA) versus their structure are studied, The stability of lathanum-APA complexes depends mainly on the number of carboxyl groups in a ligand molecule. At that, the highest stability constant is characteristic of a complex with a ligand, containing 3 nitrogen atoms and 5 carboxyl groups, in the presenoe of which the lanthanum ion coordination sphere gets satupated. The oxyethy group introduction into a ligand molecule also improves the lanthanum complex stability but to a lesser degree than during the introduction of a carboxyl group. The number of nitrogen atoms in a ligand polecule affects insignificantly the complex stability constant value, and the elongation of a chain of CH 2 groups, separating nitrogen atoms, reduces the constant to a -0.6 power

Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces

Directory of Open Access Journals (Sweden)

Krishnamoorthy Arumugam

2014-04-01

Full Text Available Applications of redox processes range over a number of scientific fields. This review article summarizes the theory behind the calculation of redox potentials in solution for species such as organic compounds, inorganic complexes, actinides, battery materials, and mineral surface-bound-species. Different computational approaches to predict and determine redox potentials of electron transitions are discussed along with their respective pros and cons for the prediction of redox potentials. Subsequently, recommendations are made for certain necessary computational settings required for accurate calculation of redox potentials. This article reviews the importance of computational parameters, such as basis sets, density functional theory (DFT functionals, and relativistic approaches and the role that physicochemical processes play on the shift of redox potentials, such as hydration or spin orbit coupling, and will aid in finding suitable combinations of approaches for different chemical and geochemical applications. Identifying cost-effective and credible computational approaches is essential to benchmark redox potential calculations against experiments. Once a good theoretical approach is found to model the chemistry and thermodynamics of the redox and electron transfer process, this knowledge can be incorporated into models of more complex reaction mechanisms that include diffusion in the solute, surface diffusion, and dehydration, to name a few. This knowledge is important to fully understand the nature of redox processes be it a geochemical process that dictates natural redox reactions or one that is being used for the optimization of a chemical process in industry. In addition, it will help identify materials that will be useful to design catalytic redox agents, to come up with materials to be used for batteries and photovoltaic processes, and to identify new and improved remediation strategies in environmental engineering, for example the

Computer analysis of potentiometric data of complexes formation in the solution

Science.gov (United States)

Jastrzab, Renata; Kaczmarek, Małgorzata T.; Tylkowski, Bartosz; Odani, Akira

2018-02-01

The determination of equilibrium constants is an important process for many branches of chemistry. In this review we provide the readers with a discussion on computer methods which have been applied for elaboration of potentiometric experimental data generated during complexes formation in solution. The review describes both: general basis of modeling tools and examples of the use of calculated stability constants.

Proceedings of the meeting on computational and experimental studies for modeling of radionuclide migration in complex aquatic ecosystems

International Nuclear Information System (INIS)

Matsunaga, Takeshi; Hakanson, Lars

2010-09-01

The Research Group for Environmental Science of JAEA held a meeting on computational and experimental studies for modeling of radionuclide migration in complex aquatic ecosystems during November 16-20 of 2009. The aim was to discuss the relevance of various computational and experimental approaches to that modeling. The meeting was attended by a Swedish researcher, Prof. Dr. Lars Hakanson of Uppsala University. It included a joint talk at the Institute for Environmental Sciences, in addition to a field and facility survey of the JNFL commercial reprocessing plant located in Rokkasho, Aomori. The meeting demonstrated that it is crucial 1) to make a model structure be strictly relevant to the target objectives of a study and 2) to account for inherent fluctuations in target values in nature in a manner of qualitative parameterization. Moreover, it was confirmed that there can be multiple different approaches of modeling (e.g. detailed or simplified) with relevance for the objectives of a study. These discussions should be considered in model integration for complex aquatic ecosystems consisting catchments, rivers, lakes and coastal oceans which can interact with the atmosphere. This report compiles research subjects and lectures presented at the meeting with associated discussions. The 10 of the presented papers indexed individually. (J.P.N.)

The impact of treatment complexity and computer-control delivery technology on treatment delivery errors

International Nuclear Information System (INIS)

Fraass, Benedick A.; Lash, Kathy L.; Matrone, Gwynne M.; Volkman, Susan K.; McShan, Daniel L.; Kessler, Marc L.; Lichter, Allen S.

1998-01-01

Purpose: To analyze treatment delivery errors for three-dimensional (3D) conformal therapy performed at various levels of treatment delivery automation and complexity, ranging from manual field setup to virtually complete computer-controlled treatment delivery using a computer-controlled conformal radiotherapy system (CCRS). Methods and Materials: All treatment delivery errors which occurred in our department during a 15-month period were analyzed. Approximately 34,000 treatment sessions (114,000 individual treatment segments [ports]) on four treatment machines were studied. All treatment delivery errors logged by treatment therapists or quality assurance reviews (152 in all) were analyzed. Machines 'M1' and 'M2' were operated in a standard manual setup mode, with no record and verify system (R/V). MLC machines 'M3' and 'M4' treated patients under the control of the CCRS system, which (1) downloads the treatment delivery plan from the planning system; (2) performs some (or all) of the machine set up and treatment delivery for each field; (3) monitors treatment delivery; (4) records all treatment parameters; and (5) notes exceptions to the electronically-prescribed plan. Complete external computer control is not available on M3; therefore, it uses as many CCRS features as possible, while M4 operates completely under CCRS control and performs semi-automated and automated multi-segment intensity modulated treatments. Analysis of treatment complexity was based on numbers of fields, individual segments, nonaxial and noncoplanar plans, multisegment intensity modulation, and pseudoisocentric treatments studied for a 6-month period (505 patients) concurrent with the period in which the delivery errors were obtained. Treatment delivery time was obtained from the computerized scheduling system (for manual treatments) or from CCRS system logs. Treatment therapists rotate among the machines; therefore, this analysis does not depend on fixed therapist staff on particular

Spinors in euclidean field theory, complex structures and discrete symmetries

International Nuclear Information System (INIS)

Wetterich, C.

2011-01-01

We discuss fermions for arbitrary dimensions and signature of the metric, with special emphasis on euclidean space. Generalized Majorana spinors are defined for d=2,3,4,8,9mod8, independently of the signature. These objects permit a consistent analytic continuation of Majorana spinors in Minkowski space to euclidean signature. Compatibility of charge conjugation with complex conjugation requires for euclidean signature a new complex structure which involves a reflection in euclidean time. The possible complex structures for Minkowski and euclidean signature can be understood in terms of a modulo two periodicity in the signature. The concepts of a real action and hermitean observables depend on the choice of the complex structure. For a real action the expectation values of all hermitean multi-fermion observables are real. This holds for arbitrary signature, including euclidean space. In particular, a chemical potential is compatible with a real action for the euclidean theory. We also discuss the discrete symmetries of parity, time reversal and charge conjugation for arbitrary dimension and signature.

Searching for new thermoelectrics in chemically and structurally complex bismuth chalcogenides

Energy Technology Data Exchange (ETDEWEB)

Chung, D Y; Hogan, T; Schindler, J; Iordanidis, L; Brazis, P; Kannewurf, C R; Chen, B; Uher, C; Kanatzidis, M G

1997-07-01

A solid state chemistry synthetic approach towards identifying new materials with potentially superior thermoelectric properties is presented. Materials with complex compositions and structures also have complex electronic structures which may give rise to high thermoelectric powers and at the same time possess low thermal conductivities. The structures and thermoelectric properties of several new promising compounds with K-Bi-Se, K-Bi-S, Ba-Bi-Te, Cs-Bi-Te, and Rb-bi-Te are reported.

Dynamic properties of epidemic spreading on finite size complex networks

Science.gov (United States)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

Optimal sensor configuration for complex systems with application to signal detection in structures

DEFF Research Database (Denmark)

Sadegh, Payman; Spall, J. C.

2000-01-01

sensor outputs. Secondly, we describe an efficient and practical algorithm to achieve the optimization goals, based on simultaneous perturbation stochastic approximation (SPSA). SPSA avoids the need for detailed modeling of the sensor response by simply relying on observed responses as obtained......The paper considers the problem of sensor configuration for complex systems. The contribution of the paper is twofold. Firstly, we define an appropriate criterion that is based on maximizing overall sensor responses while minimizing redundant information as measured by correlations between multiple...... by limited experimentation with test sensor configurations. We illustrate the application of the approach to optimal placement of acoustic sensors for signal detection in structures. This includes both a computer simulation study for an aluminum plate, and real experimentations on a steel I-beam....

Stochastic equations for complex systems theoretical and computational topics

CERN Document Server

Bessaih, Hakima

2015-01-01

Mathematical analyses and computational predictions of the behavior of complex systems are needed to effectively deal with weather and climate predictions, for example, and the optimal design of technical processes. Given the random nature of such systems and the recognized relevance of randomness, the equations used to describe such systems usually need to involve stochastics.  The basic goal of this book is to introduce the mathematics and application of stochastic equations used for the modeling of complex systems. A first focus is on the introduction to different topics in mathematical analysis. A second focus is on the application of mathematical tools to the analysis of stochastic equations. A third focus is on the development and application of stochastic methods to simulate turbulent flows as seen in reality.  This book is primarily oriented towards mathematics and engineering PhD students, young and experienced researchers, and professionals working in the area of stochastic differential equations ...

Vibrational spectroscopy and structural analysis of complex uranium compounds (review)

International Nuclear Information System (INIS)

Umreiko, D.S.; Nikanovich, M.V.

1985-01-01

The paper reports on the combined application of experimental and theoretical methods of vibrational spectroscopy together with low-temperature luminescence data to determine the characteristic features of the formation and structure of complex systems, not only containing ligands directly coordinated to the CA uranium, but also associated with the extraspherical polyatomic electrically charged particles: organic cations. These include uranyl complexes and heterocyclical amines. Studied here were compounds of tetra-halouranylates with pyridine and its derivates, as well as dipyridyl, quinoline and phenanthroline. Structural schemes are also proposed for other uranyl complexes with protonated heterocyclical amines with a more complicated composition, which correctly reflect their spectroscopic properties

Photonic crystals, light manipulation, and imaging in complex nematic structures

Science.gov (United States)

Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

2016-03-01

Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

Oligomerization of G protein-coupled receptors: computational methods.

Science.gov (United States)

Selent, J; Kaczor, A A

2011-01-01

Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

Structure and dynamics of gas phase ions: Interplay between experiments and computations in IRMPD spectroscopy

Science.gov (United States)

Coletti, Cecilia; Corinti, Davide; Paciotti, Roberto; Re, Nazzareno; Crestoni, Maria Elisa; Fornarini, Simonetta

2017-11-01

The investigation of the molecular structure and dynamics of ions in gas phase is an item of increasing interest, due the role such species play in many areas of chemistry and physics, not to mention that they often represent elusive intermediates in more complex reaction mechanisms. Infrared Multiple Photon Dissociation spectroscopy is today one of the most advanced technique to this purpose, because of its high sensitivity to even small structure changes. The interpretation of IRMPD spectra strongly relies on high level quantum mechanical computations, so that a close interplay is needed for a detailed understanding of structure and kinetics properties which can be gathered from the many applications of this powerful technique. Recent advances in experiment and theory in this field are here illustrated, with emphasis on recent progresses for the elucidation of the mechanism of action of cisplatin, one of the most widely used anticancer drugs.

Probabilistic data integration and computational complexity

Science.gov (United States)

Hansen, T. M.; Cordua, K. S.; Mosegaard, K.

2016-12-01

Inverse problems in Earth Sciences typically refer to the problem of inferring information about properties of the Earth from observations of geophysical data (the result of nature's solution to the `forward' problem). This problem can be formulated more generally as a problem of `integration of information'. A probabilistic formulation of data integration is in principle simple: If all information available (from e.g. geology, geophysics, remote sensing, chemistry…) can be quantified probabilistically, then different algorithms exist that allow solving the data integration problem either through an analytical description of the combined probability function, or sampling the probability function. In practice however, probabilistic based data integration may not be easy to apply successfully. This may be related to the use of sampling methods, which are known to be computationally costly. But, another source of computational complexity is related to how the individual types of information are quantified. In one case a data integration problem is demonstrated where the goal is to determine the existence of buried channels in Denmark, based on multiple sources of geo-information. Due to one type of information being too informative (and hence conflicting), this leads to a difficult sampling problems with unrealistic uncertainty. Resolving this conflict prior to data integration, leads to an easy data integration problem, with no biases. In another case it is demonstrated how imperfections in the description of the geophysical forward model (related to solving the wave-equation) can lead to a difficult data integration problem, with severe bias in the results. If the modeling error is accounted for, the data integration problems becomes relatively easy, with no apparent biases. Both examples demonstrate that biased information can have a dramatic effect on the computational efficiency solving a data integration problem and lead to biased results, and under

Low complexity iterative MLSE equalization in highly spread underwater acoustic channels

CSIR Research Space (South Africa)

Myburgh, HC

2009-05-01

Full Text Available methods. The superior computational complexity of the proposed equalizer is due to the high parallelism and high level of neuron interconnection of its foundational neural network structure. I. INTRODUCTION In recent years, much attention has been... are practically infeasible, as their computational complexities are exponentially related to the number of interfering symbols, rendering them computationally infeasible for UAC equaliza- tion. Attention has therefore been drawn to developing compu- tationally...

Phase behaviour and structure of stable complexes of oppositely charged polyelectrolytes

Science.gov (United States)

Mengarelli, V.; Auvray, L.; Zeghal, M.

2009-03-01

We study the formation and structure of stable electrostatic complexes between oppositely charged polyelectrolytes, a long polymethacrylic acid and a shorter polyethylenimine, at low pH, where the polyacid is weakly charged. We explore the phase diagram as a function of the charge and concentration ratio of the constituents. In agreement with theory, turbidity and ζ potential measurements show two distinct regimes of weak and strong complexation, which appear successively as the pH is increased and are separated by a well-defined limit. Weak complexes observed by neutron scattering and contrast matching have an open, non-compact structure, while strong complexes are condensed.

Digital computers in action

CERN Document Server

Booth, A D

1965-01-01

Digital Computers in Action is an introduction to the basics of digital computers as well as their programming and various applications in fields such as mathematics, science, engineering, economics, medicine, and law. Other topics include engineering automation, process control, special purpose games-playing devices, machine translation and mechanized linguistics, and information retrieval. This book consists of 14 chapters and begins by discussing the history of computers, from the idea of performing complex arithmetical calculations to the emergence of a modern view of the structure of a ge

Preparation and structural studies on organotin(IV) complexes with flavonoids

International Nuclear Information System (INIS)

Nagy, L.; Christy, A.A.; Sletten, E.; Andersen, Q.M.; Edelmann, F.T.

1998-01-01

Fourteen complexes of di-n-butyltin(IV) 2+ cations with flavonoid glycosides (rutin, hesperidin, 2',4',3-trihydroxy-5',4-dimetoxychalkone 4-rutinoside) and flavonoid aglycones (quercetin, morin, hesperitin and sorte flavones) were prepared. The composition of the complexes was determined by standard analytical methods. The results showed that complexes containing diorganotin(IV) 2+ moiety and the ligand in 1:1, 2:1 or 3:1 ratio are formed. The FTIR spectra were consistent with the presence of Sn-O (phenol or carbohydrate) vibration in the compounds. The structure of the complexes was measured by Moessbauer spectroscopy. Comparison of the experimental quadrupole splitting with those calculated on the basis of partial quadrupole splitting concept revealed that the complexes are of four types: with the central tin atoms surrounded by donor atoms in a purely trigonal-bipyramidal, octahedral+trigonal-bipyramidal, trigonal-bipyramidal+tetrahedral and octahedral+tetrahedral arrangement. This procedure also distinguished between the different structural isomers of both trigonal-bipyramidal and octahedral complexes. Conclusions could therefore be drawn on the factors determining which of the isomers are formed in the systems. The Moessbauer parameters obtained for organotin(IV)-flavonoid complexes were compared with those measured for organotin(IV)-carbohydrate complexes. (author)

Simple boron removal from seawater by using polyols as complexing agents: A computational mechanistic study

Energy Technology Data Exchange (ETDEWEB)

Kim, Min-Kyung; Eom, Ki Heon; Lim, Jun-Heok; Lee, Jea-Keun; Lee, Ju Dong; Won, Yong Sun [Pukyong National University, Busan (Korea, Republic of)

2015-11-15

The complexation of boric acid (B(OH){sub 3}), the primary form of aqueous boron at moderate pH, with polyols is proposed and mechanistically studied as an efficient way to improve membrane processes such as reverse osmosis (RO) for removing boron in seawater by increasing the size of aqueous boron compounds. Computational chemistry based on the density functional theory (DFT) was used to manifest the reaction pathways of the complexation of B(OH){sub 3} with various polyols such as glycerol, xylitol, and mannitol. The reaction energies were calculated as −80.6, −98.1, and −87.2 kcal/mol for glycerol, xylitol, and mannitol, respectively, indicating that xylitol is the most thermodynamically favorable for the complexation with B(OH){sub 3}. Moreover, the 1 : 2 molar ratio of B(OH)3 to polyol was found to be more favorable than the ratio of 1 : 1 for the complexation. Meanwhile, latest lab-scale actual RO experiments successfully supported our computational prediction that 2 moles of xylitol are the most effective as the complexing agent for 1 mole of B(OH){sub 3} in aqueous solution.

Structured Parallel Programming Patterns for Efficient Computation

CERN Document Server

McCool, Michael; Robison, Arch

2012-01-01

Programming is now parallel programming. Much as structured programming revolutionized traditional serial programming decades ago, a new kind of structured programming, based on patterns, is relevant to parallel programming today. Parallel computing experts and industry insiders Michael McCool, Arch Robison, and James Reinders describe how to design and implement maintainable and efficient parallel algorithms using a pattern-based approach. They present both theory and practice, and give detailed concrete examples using multiple programming models. Examples are primarily given using two of th

Trialkylphosphine-stabilized copper(I) gallium(III) phenylchalcogenolate complexes: crystal structures and generation of ternary semiconductors by thermolysis.

Science.gov (United States)

Kluge, Oliver; Krautscheid, Harald

2012-06-18

A series of organometallic trialkylphosphine-stabilized copper gallium phenylchalcogenolate complexes [(R(3)P)(m)Cu(n)Me(2-x)Ga(EPh)(n+x+1)] (R = Me, Et, (i)Pr, (t)Bu; E = S, Se, Te; x = 0, 1) has been prepared and structurally characterized by X-ray diffraction. From their molecular structures three groups of compounds can be distinguished: ionic compounds, ring systems, and cage structures. All these complexes contain one gallium atom bound to one or two methyl groups, whereas the number of copper atoms, and therefore the nuclearity of the complexes, is variable and depends mainly on size and amount of phosphine ligand used in synthesis. The Ga-E bonds are relatively rigid, in contrast to flexible Cu-E bonds. The lengths of the latter are controlled by the coordination number and steric influences. The Ga-E bond lengths depend systematically on the number of methyl groups bound to the gallium atom, with somewhat shorter bonds in monomethyl compounds compared to dimethyl compounds. Quantum chemical computations reproduce this trend and show furthermore that the rotation of one phenyl group around the Ga-E bond is a low energy process with two distinct minima, corresponding to two different conformations found experimentally. Mixtures of different types of chalcogen atoms on molecular scale are possible, and then ligand exchange reactions in solution lead to mixed site occupation. In thermogravimetric studies the complexes were converted into the ternary semiconductors CuGaE(2). The thermolysis reaction is completed at temperatures between 250 and 400 °C, typically with lower temperatures for the heavier chalcogens. Because of significant release of Me(3)Ga during the thermolysis process, and especially in case of copper excess in the precursor complexes, binary copper chalcogenides are obtained as additional thermolysis products. Quaternary semiconductors can be obtained from mixed chalcogen precursors.

Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives

Science.gov (United States)

Liu, Biao; Conroy, Jeffrey M.; Morrison, Carl D.; Odunsi, Adekunle O.; Qin, Maochun; Wei, Lei; Trump, Donald L.; Johnson, Candace S.; Liu, Song; Wang, Jianmin

2015-01-01

Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome. PMID:25849937

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

Science.gov (United States)

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

Computing the partition function for kinetically trapped RNA secondary structures.

Directory of Open Access Journals (Sweden)

William A Lorenz

Full Text Available An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3 time and O(n2 space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1 the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2 the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3 the (modified maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected

Prediction of Biomolecular Complexes

KAUST Repository

Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

2017-01-01

Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

Prediction of Biomolecular Complexes

KAUST Repository

Vangone, Anna

2017-04-12

Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

Optimal map of the modular structure of complex networks

International Nuclear Information System (INIS)

Arenas, A; Borge-Holthoefer, J; Gomez, S; Zamora-Lopez, G

2010-01-01

The modular structure is pervasive in many complex networks of interactions observed in natural, social and technological sciences. Its study sheds light on the relation between the structure and the function of complex systems. Generally speaking, modules are islands of highly connected nodes separated by a relatively small number of links. Every module can have the contributions of links from any node in the network. The challenge is to disentangle these contributions to understand how the modular structure is built. The main problem is that the analysis of a certain partition into modules involves, in principle, as much data as the number of modules times the number of nodes. To confront this challenge, here we first define the contribution matrix, the mathematical object containing all the information about the partition of interest, and then we use truncated singular value decomposition to extract the best representation of this matrix in a plane. The analysis of this projection allows us to scrutinize the skeleton of the modular structure, revealing the structure of individual modules and their interrelations.

8th Conference on Complex Networks

CERN Document Server

Menezes, Ronaldo; Sinatra, Roberta; Zlatic, Vinko

2017-01-01

This book collects the works presented at the 8th International Conference on Complex Networks (CompleNet) 2017 in Dubrovnik, Croatia, on March 21-24, 2017. CompleNet aims at bringing together researchers and practitioners working in areas related to complex networks. The past two decades has witnessed an exponential increase in the number of publications within this field. From biological systems to computer science, from economic to social systems, complex networks are becoming pervasive in many fields of science. It is this interdisciplinary nature of complex networks that CompleNet aims at addressing. The last decades have seen the emergence of complex networks as the language with which a wide range of complex phenomena in fields as diverse as physics, computer science, and medicine (to name a few) can be properly described and understood. This book provides a view of the state-of-the-art in this dynamic field and covers topics such as network controllability, social structure, online behavior, recommend...

The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

Science.gov (United States)

Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H-J; Lederer, H

2014-05-28

Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem

Structure of valinomycin and its complexes

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Makrlík, E.; Dušek, Michal; Císařová, I.; Dohnálek, Jan; Dušková, Jarmila; Skálová, Tereza

2009-01-01

Roč. 16, 2a (2009), s. 30-31 ISSN 1211-5894. [Struktura - Colloquium of Czech and Slovak Crystallographic Association. Hluboká nad Vltavou, 22.06.2009-25.06.2009] R&D Projects: GA ČR GA305/07/1073; GA AV ČR IAA500500701 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z10100521 Keywords : valinomycin * complex * structure 8 hydration Subject RIV: CD - Macromolecular Chemistry

Implementation of Grid-computing Framework for Simulation in Multi-scale Structural Analysis

Directory of Open Access Journals (Sweden)

Data Iranata

2010-05-01

Full Text Available A new grid-computing framework for simulation in multi-scale structural analysis is presented. Two levels of parallel processing will be involved in this framework: multiple local distributed computing environments connected by local network to form a grid-based cluster-to-cluster distributed computing environment. To successfully perform the simulation, a large-scale structural system task is decomposed into the simulations of a simplified global model and several detailed component models using various scales. These correlated multi-scale structural system tasks are distributed among clusters and connected together in a multi-level hierarchy and then coordinated over the internet. The software framework for supporting the multi-scale structural simulation approach is also presented. The program architecture design allows the integration of several multi-scale models as clients and servers under a single platform. To check its feasibility, a prototype software system has been designed and implemented to perform the proposed concept. The simulation results show that the software framework can increase the speedup performance of the structural analysis. Based on this result, the proposed grid-computing framework is suitable to perform the simulation of the multi-scale structural analysis.

The computer program system for structural design of nuclear power plants

International Nuclear Information System (INIS)

Aihara, S.; Atsumi, K.; Sasagawa, K.; Satoh, S.

1979-01-01

In recent days, the design method of the Nuclear Power Plant has become more complex than in the past. The Finite Element Method (FEM) applied for analysis of Nuclear Power Plants, especially requires more computer use. The recent computers have made remarkable progress, so that in design work manpower and time necessary for analysis have been reduced considerably. However, instead the arrangement of outputs have increased tremendously. Therefore, a computer program system was developed for performing all of the processes, from data making to output arrangement, and rebar evaluations. This report introduces the computer program system pertaining to the design flow of the Reactor Building. (orig.)

Modeling, Simulation and Analysis of Complex Networked Systems: A Program Plan for DOE Office of Advanced Scientific Computing Research

Energy Technology Data Exchange (ETDEWEB)

Brown, D L

2009-05-01

Many complex systems of importance to the U.S. Department of Energy consist of networks of discrete components. Examples are cyber networks, such as the internet and local area networks over which nearly all DOE scientific, technical and administrative data must travel, the electric power grid, social networks whose behavior can drive energy demand, and biological networks such as genetic regulatory networks and metabolic networks. In spite of the importance of these complex networked systems to all aspects of DOE's operations, the scientific basis for understanding these systems lags seriously behind the strong foundations that exist for the 'physically-based' systems usually associated with DOE research programs that focus on such areas as climate modeling, fusion energy, high-energy and nuclear physics, nano-science, combustion, and astrophysics. DOE has a clear opportunity to develop a similarly strong scientific basis for understanding the structure and dynamics of networked systems by supporting a strong basic research program in this area. Such knowledge will provide a broad basis for, e.g., understanding and quantifying the efficacy of new security approaches for computer networks, improving the design of computer or communication networks to be more robust against failures or attacks, detecting potential catastrophic failure on the power grid and preventing or mitigating its effects, understanding how populations will respond to the availability of new energy sources or changes in energy policy, and detecting subtle vulnerabilities in large software systems to intentional attack. This white paper outlines plans for an aggressive new research program designed to accelerate the advancement of the scientific basis for complex networked systems of importance to the DOE. It will focus principally on four research areas: (1) understanding network structure, (2) understanding network dynamics, (3) predictive modeling and simulation for complex

Modeling, Simulation and Analysis of Complex Networked Systems: A Program Plan for DOE Office of Advanced Scientific Computing Research

International Nuclear Information System (INIS)

Brown, D.L.

2009-01-01

Many complex systems of importance to the U.S. Department of Energy consist of networks of discrete components. Examples are cyber networks, such as the internet and local area networks over which nearly all DOE scientific, technical and administrative data must travel, the electric power grid, social networks whose behavior can drive energy demand, and biological networks such as genetic regulatory networks and metabolic networks. In spite of the importance of these complex networked systems to all aspects of DOE's operations, the scientific basis for understanding these systems lags seriously behind the strong foundations that exist for the 'physically-based' systems usually associated with DOE research programs that focus on such areas as climate modeling, fusion energy, high-energy and nuclear physics, nano-science, combustion, and astrophysics. DOE has a clear opportunity to develop a similarly strong scientific basis for understanding the structure and dynamics of networked systems by supporting a strong basic research program in this area. Such knowledge will provide a broad basis for, e.g., understanding and quantifying the efficacy of new security approaches for computer networks, improving the design of computer or communication networks to be more robust against failures or attacks, detecting potential catastrophic failure on the power grid and preventing or mitigating its effects, understanding how populations will respond to the availability of new energy sources or changes in energy policy, and detecting subtle vulnerabilities in large software systems to intentional attack. This white paper outlines plans for an aggressive new research program designed to accelerate the advancement of the scientific basis for complex networked systems of importance to the DOE. It will focus principally on four research areas: (1) understanding network structure, (2) understanding network dynamics, (3) predictive modeling and simulation for complex networked systems

[The P300-based brain-computer interface: presentation of the complex "flash + movement" stimuli].

Science.gov (United States)

Ganin, I P; Kaplan, A Ia

2014-01-01

The P300 based brain-computer interface requires the detection of P300 wave of brain event-related potentials. Most of its users learn the BCI control in several minutes and after the short classifier training they can type a text on the computer screen or assemble an image of separate fragments in simple BCI-based video games. Nevertheless, insufficient attractiveness for users and conservative stimuli organization in this BCI may restrict its integration into real information processes control. At the same time initial movement of object (motion-onset stimuli) may be an independent factor that induces P300 wave. In current work we checked the hypothesis that complex "flash + movement" stimuli together with drastic and compact stimuli organization on the computer screen may be much more attractive for user while operating in P300 BCI. In 20 subjects research we showed the effectiveness of our interface. Both accuracy and P300 amplitude were higher for flashing stimuli and complex "flash + movement" stimuli compared to motion-onset stimuli. N200 amplitude was maximal for flashing stimuli, while for "flash + movement" stimuli and motion-onset stimuli it was only a half of it. Similar BCI with complex stimuli may be embedded into compact control systems requiring high level of user attention under impact of negative external effects obstructing the BCI control.

Thermodynamics and Structure of Actinide(IV) Complexes with Nitrilotriacetic Acid

Energy Technology Data Exchange (ETDEWEB)