Journal articles: 'Complete computational structure'

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Aleksandrowicz, Gadi, Hana Chockler, Joseph Y. Halpern, and Alexander Ivrii. "The Computational Complexity of Structure-Based Causality." Journal of Artificial Intelligence Research 58 (February 27, 2017): 431–51. http://dx.doi.org/10.1613/jair.5229.

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Halpern and Pearl introduced a definition of actual causality; Eiter and Lukasiewicz showed that computing whether X = x is a cause of Y = y is NP-complete in binary models (where all variables can take on only two values) and Σ^P_2 -complete in general models. In the final version of their paper, Halpern and Pearl slightly modified the definition of actual cause, in order to deal with problems pointed out by Hopkins and Pearl. As we show, this modification has a nontrivial impact on the complexity of computing whether {X} = {x} is a cause of Y = y. To characterize the complexity, a new family D_k^P , k = 1, 2, 3, . . ., of complexity classes is introduced, which generalises the class DP introduced by Papadimitriou and Yannakakis (DP is just D_1^P). We show that the complexity of computing causality under the updated definition is D_2^P -complete. Chockler and Halpern extended the definition of causality by introducing notions of responsibility and blame, and characterized the complexity of determining the degree of responsibility and blame using the original definition of causality. Here, we completely characterize the complexity using the updated definition of causality. In contrast to the results on causality, we show that moving to the updated definition does not result in a difference in the complexity of computing responsibility and blame.

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Adolf-Bryfogle, Jared, Frank D. Teets, and Christopher D. Bahl. "Toward complete rational control over protein structure and function through computational design." Current Opinion in Structural Biology 66 (February 2021): 170–77. http://dx.doi.org/10.1016/j.sbi.2020.10.015.

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BERGMAN, CLIFFORD, and GIORA SLUTZKI. "COMPUTATIONAL COMPLEXITY OF GENERATORS AND NONGENERATORS IN ALGEBRA." International Journal of Algebra and Computation 12, no. 05 (October 2002): 719–35. http://dx.doi.org/10.1142/s0218196702001127.

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We discuss the computational complexity of several problems concerning subsets of an algebraic structure that generate the structure. We show that the problem of determining whether a given subset X generates an algebra A is P-complete, while determining the size of the smallest generating set is NP-complete. We also consider several questions related to the Frattini subuniverse, Φ(A), of an algebra A. We show that the membership problem for Φ(A) is co-NP-complete, while the membership problems for Φ(Φ(A)), Φ(Φ(Φ(A))),… all lie in the class P‖(NP).

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Vejdemo-Johansson, Mikael. "Blackbox computation of A ∞-algebras." gmj 17, no. 2 (June 2010): 391–404. http://dx.doi.org/10.1515/gmj.2010.005.

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Abstract Kadeishvili's proof of theminimality theorem [T. Kadeishvili, On the homology theory of fiber spaces, Russ. Math. Surv. 35:3 (1980), 231–238] induces an algorithm for the inductive computation of an A ∞-algebra structure on the homology of a dg-algebra. In this paper, we prove that for one class of dg-algebras, the resulting computation will generate a complete A ∞-algebra structure after a finite amount of computational work.

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Golod, V. M., and L. Yu Dobosh. "DIAGNOSTICS OF DENDRITE STRUCTURE OF MULTICOMPONENT ALUMINUM ALLOYS." Litiyo i Metallurgiya (FOUNDRY PRODUCTION AND METALLURGY), no. 1 (April 6, 2018): 55–62. http://dx.doi.org/10.21122/1683-6065-2018-1-55-62.

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Stages of system analysis and mathematical models for predicting the dendritic structure of multicomponent aluminum alloys are considered. Computer diagnostics of nonequilibrium crystallization is realized by the joint use of the apparatus of computational thermodynamics and means of computational heat transfer for solving problems of computational materials science. The results of modeling the evolution of the dendritic structure are presented with a change in the diffusion intensity in the solid phase from equilibrium conditions to complete suppression.

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FU, YUXI. "Non-deterministic structures of computation." Mathematical Structures in Computer Science 25, no. 6 (November 10, 2014): 1295–338. http://dx.doi.org/10.1017/s0960129514000012.

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Divergence and non-determinism play a fundamental role in the theory of computation, and their combined effect on computational equality deserves further study. By looking at the issue from the point of view of both computation and interaction, we are led to a canonical equality for non-deterministic computation, revealing its rich algebraic structure. We study this structure in three ways. First, we construct a complete equational system for finite-state non-deterministic computation. The challenge with such a system is to find an equational alternative to fixpoint inductionà laMilner. We establish a negative result in the form of the non-existence of a finite equational system for the canonical equality of non-deterministic computation to support our approach. We then investigate infinite-state non-deterministic computation in the light of definability and show that every recursively enumerable set is generated by an unobservable process. Finally, we prove that, as far as computation is concerned, the effect produced jointly by divergence and non-determinism is model independent for a large class of process models.We use C-graphs, which are interesting in their own right, as abstract representations of the computational objects throughout the paper.

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Sobczyk, Kamil, Ryszard Chmielewski, and Krzysztof Duda. "The concept of a prefabricated structure for protection of critical infrastructure facilities." Bulletin of the Military University of Technology 67, no. 2 (June 29, 2018): 133–44. http://dx.doi.org/10.5604/01.3001.0012.0979.

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The paper presents the concept of a protective structure in the form of a prefabricated reinforced concrete protective dome intended for protection of a single critical infrastructure facility [1]. Unlike non-movable cast-in-place reinforced concrete structures, the protective structure can be assembled and disassembled repeatedly with the use of dedicated joining sockets. To provide the concept with a high mobility, the dimensions of single modules of the prefabricated reinforced concrete protective dome meet the transport limits dictated by the horizontal and vertical clearance of roads. A numerical computational analysis facilitated a determination of the distribution of internal forces in the protective stricture and dimensioning of the required reinforcement system [3]. The computations included standardized cases of steady and dynamic loads, and combinations thereof, complete with parameters of dynamic loads from an explosion impulse. Keywords: building engineering, protective structure, prefabricated dome

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Song, Bosheng, and Yuan Kong. "Solution to PSPACE-Complete Problem Using P Systems with Active Membranes with Time-Freeness." Mathematical Problems in Engineering 2019 (June 27, 2019): 1–8. http://dx.doi.org/10.1155/2019/5793234.

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P systems with active membranes are powerful parallel natural computing models, which were inspired by cell structure and behavior. Inspired by the parallel processing of biological information and with the idealistic assumption that each rule is completed in exactly one time unit, P systems with active membranes are able to solve computational hard problems in a feasible time. However, an important biological fact in living cells is that the execution time of a biochemical reaction cannot be accurately divided equally and completed in one time unit. In this work, we consider time as an important factor for the computation in P systems with active membranes and investigate the computational efficiency of such P systems. Specifically, we present a time-free semiuniform solution to the quantified Boolean satisfiability problem (QSATproblem, for short) in the framework of P systems with active membranes, where the solution to such problem is correct, which does not depend on the execution time for the used rules.

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Dinneen, Michael J., Yun-Bum Kim, and Radu Nicolescu. "Towards Structured Modelling with Hyperdag P Systems." International Journal of Computers Communications & Control 5, no. 2 (June 1, 2010): 224. http://dx.doi.org/10.15837/ijccc.2010.2.2477.

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Although P systems are computationally complete, many real world models, such as socio-economic systems, databases, operating systems and distributed systems, seem to require more expressive power than provided by tree structures. Many such systems have a primary tree-like structure augmented with shared or secondary communication channels. Modelling these as tree-based systems, while theoretically possible, is not very appealing, because it typically needs artificial extensions that introduce additional complexities, inexistent in the originals. In this paper, we propose and define a new model called hyperdag P systems, in short, hP systems, which extend the definition of conventional P systems, by allowing dags, interpreted as hypergraphs, instead of trees, as models for the membrane structure. We investigate the relation between our hP systems and neural P systems. Despite using an apparently restricted structure, i.e., a dag instead of a general graph, we argue that hP systems have essentially the same computational power as tissue and neural P systems. We argue that hP systems offer a structured approach to membranebased modelling that is often closer to the behavior and underlying structure of the modelled objects.

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Sadowski, Michał. "Topological structure of complete Riemannian manifolds with cyclic holonomy groups." Differential Geometry and its Applications 23, no. 2 (September 2005): 106–13. http://dx.doi.org/10.1016/j.difgeo.2005.05.003.

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11

Joret, Gwenaël, and David R. Wood. "Complete graph minors and the graph minor structure theorem." Journal of Combinatorial Theory, Series B 103, no. 1 (January 2013): 61–74. http://dx.doi.org/10.1016/j.jctb.2012.09.001.

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12

Noviello, Teresa Maria Rosaria, Francesco Ceccarelli, Michele Ceccarelli, and Luigi Cerulo. "Deep learning predicts short non-coding RNA functions from only raw sequence data." PLOS Computational Biology 16, no. 11 (November 11, 2020): e1008415. http://dx.doi.org/10.1371/journal.pcbi.1008415.

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Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is determinant to know RNA function and machine learning based approaches have been successfully proven to predict RNA function from secondary structure information. Here we show that RNA function can be predicted with good accuracy from a lightweight representation of sequence information without the necessity of computing secondary structure features which is computationally expensive. This finding appears to go against the dogma of secondary structure being a key determinant of function in RNA. Compared to recent secondary structure based methods, the proposed solution is more robust to sequence boundary noise and reduces drastically the computational cost allowing for large data volume annotations. Scripts and datasets to reproduce the results of experiments proposed in this study are available at: https://github.com/bioinformatics-sannio/ncrna-deep.

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13

Smith, Kevin. "On complete interpolating sequences and sampling expansions." LMS Journal of Computation and Mathematics 13 (February 2, 2010): 1–9. http://dx.doi.org/10.1112/s146115700700037x.

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AbstractComplete interpolating sequences forL2(−π,π) are considered under the condition that the real parts of the sequence are a subsequence of the scaled integersx,x>0. It is found that this condition leads to very specific and restrictive conditions on the existence and structure of complete interpolating sequences forL2(−π,π). Further general results in the case of bunched sampling of Bernstein functions are also given.

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14

Sutcliffe, Mike. "Relationship between protein structure and function: Valuable insight from computational studies." Biochemist 26, no. 4 (August 1, 2004): 13–16. http://dx.doi.org/10.1042/bio02604013.

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Life as we know it is sustained by the plethora of functional roles performed by proteins -- the precise function depending exquisitely on three-dimensional structure. The quest to understand protein function from structure has led worldwide to the establishment of a number of structural genomics projects and the concomitant substantial investment from both the public and private sectors, estimated to total around US$1 billion worldwide. Once a structure is solved, deducing function on the basis of this structure alone is often a non-trivial, but nonetheless essential, exercise -- mankind's pursuit of a complete, working molecular model of a cell is underway. This article discusses some of the computational approaches that assist in: (i) deducing function from protein structure, and (ii) elucidating factors at the atomic level that determine function. Far from replacing experimental studies, these approaches should be used to complement them -- the real value comes from an interdependent multidisciplinary approach.

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15

Worden, Keith, and Graeme Manson. "Prognosis under Uncertainty – An Idealised Computational Case Study." Shock and Vibration 15, no. 3-4 (2008): 231–43. http://dx.doi.org/10.1155/2008/958343.

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The object of this paper is to investigate computationally the possibility of damage prognosis in a structure under the most idealised circumstances. A simple isotropic material – Titanium alloy Ti-6Al-4V – is assumed. The structure is a simple finite plate under harmonic uniaxial loading and the damage is assumed to be a central mode 1 through crack for which various approximations to the stress intensity factor are known. The damage propagation model is the Paris-Erdogan law. Where the paper departs from complete simplicity is in the assumption that the parameters of the damage propagation law are uncertain. The paper investigates the effect of the parameter uncertainty on the estimated lifetime of the specimen. Two approaches are adopted for the uncertainty propagation, a statistical Monte Carlo scheme and one based on interval arithmetic.

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Ravaioli, U., A. Duncan, A. Pacelli, C. Wordelman, and K. Hess. "Hierarchy of Full Band Structure Models for Monte Carlo Simulation." VLSI Design 6, no. 1-4 (January 1, 1998): 147–53. http://dx.doi.org/10.1155/1998/16901.

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This paper discusses the various hierarchy levels that are possible when the full band structure is considered. At the highest level, the scatterings are treated using complete k-k’ transition rates, which entail extremely memory intensive computational applications. At the lowest level, the scattering anisotropy is neglected and the scattering rate is considered to be a constant average value on energy isosurfaces of the bandstructure. This model is more practical for device simulation. In between the two extremes, it is possible to design intermediate models which preserve some essential features of both. At all levels of the band structure hierarchy of models, there are similar issues of numerical noise, related to the sampling of real and momentum space that the Monte Carlo method necessarily performs with a relatively small number of particles. We discuss here computationally efficient approaches based on the assignment of variable weights to the simulated particles, in conjunction with careful gatherscatter procedures to split particles of large weight and combine particles of small weight.

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Garrison, C. J. "A Numerically Efficient Method for Analysis of Very Large Articulated Floating Structures." Journal of Ship Research 42, no. 03 (September 1, 1998): 174–86. http://dx.doi.org/10.5957/jsr.1998.42.3.174.

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A method is presented for evaluation of the motion of long structures composed of interconnected barges, or modules, of arbitrary shape. Such structures are being proposed in the construction of offshore airports or other large offshore floating structures. It is known that the evaluation of the motion of jointed or otherwise interconnected modules which make up a long floating structure may be evaluated by three dimensional radiation/diffraction analysis. However, the computing effort increases rapidly as the complexity of the geometric shape of the individual modules and the total number of modules increases. This paper describes an approximate method which drastically reduces the computational effort without major effects on accuracy. The method relies on accounting for hydrodynamic interaction effects between only adjacent modules within the structure rather than between all of the modules since the near-field interaction is by far the more important. This approximation reduces the computational effort to that of solving the two-module problem regardless of the total number of modules in the complete structure.

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Bespalova, E. I., and I. K. Senchenkov. "Analysis of spatial structure elements from elastomer materials by methods of complete systems." Soviet Applied Mechanics 26, no. 12 (December 1990): 1115–18. http://dx.doi.org/10.1007/bf00887671.

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Voice, T., M. Polukarov, and N. R. Jennings. "Coalition Structure Generation over Graphs." Journal of Artificial Intelligence Research 45 (October 19, 2012): 165–96. http://dx.doi.org/10.1613/jair.3715.

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We give the analysis of the computational complexity of coalition structure generation over graphs. Given an undirected graph G = (N,E) and a valuation function v : P(N) → R over the subsets of nodes, the problem is to find a partition of N into connected subsets, that maximises the sum of the components values. This problem is generally NPcomplete; in particular, it is hard for a defined class of valuation functions which are independent of disconnected membersthat is, two nodes have no effect on each others marginal con- tribution to their vertex separator. Nonetheless, for all such functions we provide bounds on the complexity of coalition structure generation over general and minorfree graphs. Our proof is constructive and yields algorithms for solving corresponding instances of the problem. Furthermore, we derive linear time bounds for graphs of bounded treewidth. However, as we show, the problem remains NPcomplete for planar graphs, and hence, for any K_k minorfree graphs where k ≥ 5. Moreover, a 3-SAT problem with m clauses can be represented by a coalition structure generation problem over a planar graph with O(m^2) nodes. Importantly, our hardness result holds for a particular subclass of valuation functions, termed edge sum, where the value of each subset of nodes is simply determined by the sum of given weights of the edges in the induced subgraph.

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Wu, Qian, Biao Hou, Zaidao Wen, Zhongle Ren, Bo Ren, and Licheng Jiao. "Structure Label Matrix Completion for PolSAR Image Classification." Remote Sensing 12, no. 3 (February 1, 2020): 459. http://dx.doi.org/10.3390/rs12030459.

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Terrain classification is a hot topic in polarimetric synthetic aperture radar (PolSAR) image interpretation that aims at assigning a label to every pixel and forms a label matrix for a PolSAR image. From the perspective of human interpretation, classification is not in terms of pixels, but decomposed perceptual groups and structures. Therefore, a new perspective of label matrix completion is proposed to treat the classification task as a label matrix inversion process. Firstly, a matrix completion framework is built to avoid processing the large-scale PolSAR image data for traditional feature and classifier learning. Secondly, a light network is used to obtain the known labels for the complete task by uniform down-sampling of the entire image that aims to keep the shape of regions in a PolSAR image and reduce the computational complexity. Finally, the zeroth- and first-order label information is proposed as the prior distribution for label matrix completion to keep the structure and texture. The experiments are tested on real PolSAR images, which demonstrates that the proposed method can realize excellent classification results with less computation time and labeled pixels. Classification results with different down-sampling rates in the light network also prove the robustness of this method.

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Janardhanan, S., and Saurabh Inamdar. "Computationally Efficient Functional Observer for LTI System Based on a Multirate Output Sampling Algorithm." Advanced Materials Research 403-408 (November 2011): 3875–83. http://dx.doi.org/10.4028/www.scientific.net/amr.403-408.3875.

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This paper proposes a technique for computing a vector linear functional of the system states of a linear time invariant (LTI) system. The concept of multirate output observations has been used to design the observer. The paper also proves that the complete state observability of a system is not a necessary condition for the existence of a functional observer. The proposed technique reduces the computational time and complexity of the hardware and software of the observer system considerably due to static structure of observer as well as involvement of reduced dimension matrices in computation of the functional. The proposed technique has been validated using numerical examples.

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Pisano, Aurora Angela, and Paolo Fuschi. "Structural symmetry within nonlocal integral elasticity: theoretical issues and computational strategies." Curved and Layered Structures 4, no. 1 (January 26, 2017): 1–7. http://dx.doi.org/10.1515/cls-2017-0001.

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Abstract The structural symmetry and the appropriate definition of a reduced (symmetric) mechanical/ numerical model is discussed within a nonlocal elasticity context. In particular, reference is made to an integral model of Eringen-type. The paper highlights how the classical, i.e. local, concepts of structural symmetry have to be rephrased through the definition of an enlarged symmetric model of the analyzed structure. This enlarged model, endowed with apposite nonlocal boundary conditions enforced in an iterative fashion, is proved to be able to recover the nonlocal effects that the neglected portion of the structure exerts on the portion chosen for the analysis. It is shown how the mirrored symmetric solution exactly matches the complete one. Theoretical issues and computational strategies referred to a nonlocal version of the finite element method are discussed with reference to the analysis of a case-study.

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Garcia-Saez, Artur, and Jose I. Latorre. "An exact tensor network for the 3SAT problem." Quantum Information and Computation 12, no. 3&4 (March 2012): 283–92. http://dx.doi.org/10.26421/qic12.3-4-8.

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We construct a tensor network that delivers an unnormalized quantum state whose coefficients are the solutions to a given instance of 3SAT, an NP-complete problem. The tensor network contraction that corresponds to the norm of the state counts the number of solutions to the instance. It follows that exact contractions of this tensor network are in the \#P-complete computational complexity class, thus believed to be a hard task. Furthermore, we show that for a 3SAT instance with $n$ bits, it is enough to perform a polynomial number of contractions of the tensor network structure associated to the computation of local observables to obtain one of the explicit solutions to the problem, if any. Physical realization of a state described by a generic tensor network is equivalent to finding the satisfying assignment of a 3SAT instance and, consequently, this experimental task is expected to be hard.

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Schlecht, Sebastian J. "Frequency-Dependent Schroeder Allpass Filters." Applied Sciences 10, no. 1 (December 25, 2019): 187. http://dx.doi.org/10.3390/app10010187.

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Since the introduction of feedforward–feedback comb allpass filters by Schroeder and Logan, its popularity has not diminished due to its computational efficiency and versatile applicability in artificial reverberation, decorrelation, and dispersive system design. In this work, we present an extension to the Schroeder allpass filter by introducing frequency-dependent feedforward and feedback gains while maintaining the allpass characteristic. By this, we directly improve upon the design of Dahl and Jot which exhibits a frequency-dependent absorption but does not preserve the allpass property. At the same time, we also improve upon Gerzon’s allpass filter as our design is both less restrictive and computationally more efficient. We provide a complete derivation of the filter structure and its properties. Furthermore, we illustrate the usefulness of the structure by designing an allpass decorrelation filter with frequency-dependent decay characteristics.

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Bermejo, Mario, Anastasio P. Santos, and José M. Goicolea. "Development of Practical Finite Element Models for Collapse of Reinforced Concrete Structures and Experimental Validation." Shock and Vibration 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/4636381.

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This paper describes two practical methodologies for modeling the collapse of reinforced concrete structures. They are validated with a real scale test of a two-floor structure which loses a bearing column. The objective is to achieve accurate simulations of collapse phenomena with moderate computational cost. Explicit finite element models are used with Lagrangian meshes, modeling concrete, and steel in a segregated manner. The first model uses 3D continuum finite elements for concrete and beams for steel bars, connected for displacement compatibility using a penalty method. The second model uses structural finite elements, shells for concrete, and beams for steel, connected in common nodes with an eccentricity formulation. Both are capable of simulating correctly the global behavior of the structural collapse. The continuum finite element model is more accurate for interpreting local failure but has an excessive computational cost for a complete building. The structural finite element model proposed has a moderate computational cost, yields sufficiently accurate results, and as a result is the recommended methodology.

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Fine, C., and R. J. R. Blair. "Computations in extraversion." Behavioral and Brain Sciences 22, no. 3 (June 1999): 521–23. http://dx.doi.org/10.1017/s0140525x99262048.

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We make two suggestions with regard to Depue & Collins's (D&C's) target article. First, regarding the functioning of MOC13, we provide data indicating that, contrary to D&C's apparent position, this structure is not necessary for instrumental conditioning. Second, we suggest that D&C's approach would be advanced by reference to formal computational theory, in particular the work of Grossberg. We suggest that an integration of Grossberg's and D&C's models can provide a more complete account of extraversion.

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Zhao, Wei Tao, Feng Guo, and Xiao Li. "Reliability Analysis of Composite Structure Using ANSYS Software." Advanced Materials Research 945-949 (June 2014): 1155–58. http://dx.doi.org/10.4028/www.scientific.net/amr.945-949.1155.

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ANSYS software has provided complete and accurate solutions for composite laminate analysis and provided a set of special elements for different composite structures such as laminated plates, beams, solid structures and stiffeners. Fiber composite materials have been widely used to critical components of aircrafts, automobiles, mechanical, and marine structures. Since uncertainties associated with geometric tolerances, material properties, and boundary conditions widely exist in practical engineering problems. The probability approach is the most popular way to quantify uncertain parameters and perform the reliability analysis. The paper researches on the reliability analysis of the composite panels using ANSYS software. The numerical example is given, it is shown that the response surface method (RSM) can reduce the computational efforts comparing with Monte Carlo simulation (MCS).

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Chang, Xing Yang, Qi Shen, Wen Xue Fan, and Hai Hao. "Optimization of Magnesium Alloy Casting Process: An Integrated Computational Materials Engineering (ICME) Approach." Materials Science Forum 1035 (June 22, 2021): 808–12. http://dx.doi.org/10.4028/www.scientific.net/msf.1035.808.

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Traditional casting process optimization usually adopts empirical trial and error method. Process parameters were modified repeatedly within a certain range until a satisfactory solution is obtained, which is costly and inefficient. Therefore, based on integrated computational materials engineering, Magnesium Alloy Simulation Integrated Platform (MASIP) was constructed. MASIP completed the automatic operation of the entire simulation process from the CAD model data input to the process-microstructure-performance. It realized the rapid optimization simulation prediction of process-microstructure-performance, and solved the problems of long cycle and low efficiency of traditional process optimization. This paper studied the low-pressure casting optimization process of magnesium alloy thin-walled cylindrical parts based on MASIP. The calculation took casting temperature, mold temperature and holding pressure as the optimized variables, and the yield strength of the casting as the target variable. The experimental results showed that MASIP can fairly complete the structure simulation and performance prediction of castings, greatly reduce the time cost of the calculation process, and improve the efficiency of process optimization.

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Cussens, James, Matti Järvisalo, Janne H. Korhonen, and Mark Bartlett. "Bayesian Network Structure Learning with Integer Programming: Polytopes, Facets and Complexity." Journal of Artificial Intelligence Research 58 (January 26, 2017): 185–229. http://dx.doi.org/10.1613/jair.5203.

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The challenging task of learning structures of probabilistic graphical models is an important problem within modern AI research. Recent years have witnessed several major algorithmic advances in structure learning for Bayesian networks - arguably the most central class of graphical models - especially in what is known as the score-based setting. A successful generic approach to optimal Bayesian network structure learning (BNSL), based on integer programming (IP), is implemented in the GOBNILP system. Despite the recent algorithmic advances, current understanding of foundational aspects underlying the IP based approach to BNSL is still somewhat lacking. Understanding fundamental aspects of cutting planes and the related separation problem is important not only from a purely theoretical perspective, but also since it holds out the promise of further improving the efficiency of state-of-the-art approaches to solving BNSL exactly. In this paper, we make several theoretical contributions towards these goals: (i) we study the computational complexity of the separation problem, proving that the problem is NP-hard; (ii) we formalise and analyse the relationship between three key polytopes underlying the IP-based approach to BNSL; (iii) we study the facets of the three polytopes both from the theoretical and practical perspective, providing, via exhaustive computation, a complete enumeration of facets for low-dimensional family-variable polytopes; and, furthermore, (iv) we establish a tight connection of the BNSL problem to the acyclic subgraph problem.

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BOTTONI, PAOLO, DANIELE GORLA, STEFANO KASANGIAN, and ANNA LABELLA. "A doctrinal approach to modal/temporal Heyting logic and non-determinism in processes." Mathematical Structures in Computer Science 28, no. 4 (February 27, 2017): 508–32. http://dx.doi.org/10.1017/s0960129517000019.

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The study of algebraic modelling of labelled non-deterministic concurrent processes leads us to consider a category LB, obtained from a complete meet-semilattice B and from B-valued equivalence relations. We prove that, if B has enough properties, then LB presents a two-fold internal logical structure, induced by two doctrines definable on it: one related to its families of subobjects and one to its families of regular subobjects. The first doctrine is Heyting and makes LB a Heyting category, the second one is Boolean. We will see that the difference between these two logical structures, namely the different behaviour of the negation operator, can be interpreted in terms of a distinction between non-deterministic and deterministic behaviours of agents able to perform computations in the context of the same process. Moreover, the sorted first-order logic naturally associated with LB can be extended to a modal/temporal logic, again using the doctrinal setting. Relations are also drawn to other computational models.

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Wiederstein, Markus, and Manfred J. Sippl. "TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D." Nucleic Acids Research 48, W1 (June 1, 2020): W31—W35. http://dx.doi.org/10.1093/nar/gkaa366.

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Abstract Frequently, the complete functional units of biological molecules are assemblies of protein and nucleic acid chains. Stunning examples are the complex structures of ribosomes. Here, we present TopMatch-web, a computational tool for the study of the three-dimensional structure, function and evolution of such molecules. The unique feature of TopMatch is its ability to match the protein as well as nucleic acid chains of complete molecular assemblies simultaneously. The resulting structural alignments are visualized instantly using the high-performance molecular viewer NGL. We use the mitochondrial ribosomes of human and yeast as an example to demonstrate the capabilities of TopMatch-web. The service responds immediately, enabling the interactive study of many pairwise alignments of large molecular assemblies in a single session. TopMatch-web is freely accessible at https://topmatch.services.came.sbg.ac.at.

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Alladi, Subha Mahadevi. "Advances in Computational Studies of Potential Drug Targets in Mycobacterium tuberculosis." Current Topics in Medicinal Chemistry 18, no. 13 (October 4, 2018): 1062–74. http://dx.doi.org/10.2174/1568026618666180806163428.

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Tuberculosis continues to remain as one of the leading causes of death worldwide, in spite of significant progress being made in the last twenty years through increased compliance to treatment. The current review gives an overview of the recent efforts made in the endeavor to identify novel inhibitors and promising drug targets for Mycobacterium tuberculosis with structure and ligand-based approaches along with bioinformatics studies following complete sequencing of its genome. A large number of these studies target biomolecules in metabolic pathways that are vital for the survival of the microorganism. A discussion on efforts to study metalloproteins as relatively underexplored targets in the context of their druggability is also presented.

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Erkol, Şirag, and Gönenç Yücel. "Influence maximization based on partial network structure information: A comparative analysis on seed selection heuristics." International Journal of Modern Physics C 28, no. 10 (October 2017): 1750122. http://dx.doi.org/10.1142/s0129183117501224.

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In this study, the problem of seed selection is investigated. This problem is mainly treated as an optimization problem, which is proved to be NP-hard. There are several heuristic approaches in the literature which mostly use algorithmic heuristics. These approaches mainly focus on the trade-off between computational complexity and accuracy. Although the accuracy of algorithmic heuristics are high, they also have high computational complexity. Furthermore, in the literature, it is generally assumed that complete information on the structure and features of a network is available, which is not the case in most of the times. For the study, a simulation model is constructed, which is capable of creating networks, performing seed selection heuristics, and simulating diffusion models. Novel metric-based seed selection heuristics that rely only on partial information are proposed and tested using the simulation model. These heuristics use local information available from nodes in the synthetically created networks. The performances of heuristics are comparatively analyzed on three different network types. The results clearly show that the performance of a heuristic depends on the structure of a network. A heuristic to be used should be selected after investigating the properties of the network at hand. More importantly, the approach of partial information provided promising results. In certain cases, selection heuristics that rely only on partial network information perform very close to similar heuristics that require complete network data.

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Bettinger, Holger F. "Electronic structure of higher acenes and polyacene: The perspective developed by theoretical analyses." Pure and Applied Chemistry 82, no. 4 (March 20, 2010): 905–15. http://dx.doi.org/10.1351/pac-con-09-10-29.

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The hypothetical polymer obtained by linear annelation of benzene units, polyacene (PAC) (C4H2)n, has received considerable attention over the last 50 years. This interest is due to the unusual electronic structure that is assumed to result in usual physical properties. The review summarizes the theoretical investigations of PAC research. The most recent computational analyses available in the literature are based on density functional theory (DFT) for PAC and on the complete active space self-consistent field (CASSCF) method for oligoacenes and suggest an undistorted symmetrical structure with an antiferromagnetic (AFM) coupling of electrons.

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Granifo, Juan, Rubén Gaviño, Sebastián Suárez, and Ricardo Baggio. "Structural characterization of a hybrid terpyridine–pyrazine ligand and its one-dimensional ZnII coordination polymer: a computational approach to conventional and nonconventional intermolecular interactions." Acta Crystallographica Section C Structural Chemistry 75, no. 9 (August 20, 2019): 1299–309. http://dx.doi.org/10.1107/s2053229619011161.

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The structures of a new hybrid terpyridine–pyrazine ligand, namely 4′-[4-(pyrazin-2-yl)phenyl]-4,2′:6′,4′′-terpyridine (L2), C25H17N5, and its one-dimensional coordination polymer catena-poly[[bis(acetylacetonato-κ2 O,O′)zinc]-μ-4′-[4-(pyrazin-2-yl-κN 4)phenyl]-4,2′:6′,4′′-terpyridine-κN 1], [Zn(C5H7O2)2(C25H17N5)] n or [Zn(acac)2(L2)] n (Hacac is acetylacetone), are reported. Packing interactions in both crystal structures are analyzed using Hirshfeld surface and enrichment ratio techniques. For the simpler structure of the monomeric ligand, further studies on the interaction hierarchy using the energy framework approach were made. The result was a complete picture of the intermolecular interaction landscape, which revealed some subtle details, for example, that some weak (at first sight negligible) C—H...N interactions in the structure of free L2 play a relevant role in the crystal stabilization.

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Wang, F., H. Mackenzie-Ross, D. A. Winkler, I. E. McCarthy, L. Campbell, and M. J. Brunger. "A high-resolution electron momentum spectroscopy and density functional theory study into the complete valence electronic structure of allene." Journal of Computational Chemistry 22, no. 13 (2001): 1321–33. http://dx.doi.org/10.1002/jcc.1090.

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Bourke, Jay D., Christopher T. Chantler, and Yves Joly. "FDMX: extended X-ray absorption fine structure calculations using the finite difference method." Journal of Synchrotron Radiation 23, no. 2 (February 18, 2016): 551–59. http://dx.doi.org/10.1107/s1600577516001193.

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A new theoretical approach and computational package,FDMX, for general calculations of X-ray absorption fine structure (XAFS) over an extended energy range within a full-potential model is presented. The final-state photoelectron wavefunction is calculated over an energy-dependent spatial mesh, allowing for a complete representation of all scattering paths. The electronic potentials and corresponding wavefunctions are subject to constraints based on physicality and self-consistency, allowing for accurate absorption cross sections in the near-edge region, while higher-energy results are enabled by the implementation of effective Debye–Waller damping and new implementations of second-order lifetime broadening. These include inelastic photoelectron scattering and, for the first time, plasmon excitation coupling. This is the first full-potential package available that can calculate accurate XAFS spectra across a complete energy range within a single framework and without fitted parameters. Example spectra are provided for elemental Sn, rutile TiO2and the FeO6octahedron.

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KAPOOR, SANJIV, and XIANG-YANG LI. "PROXIMITY STRUCTURES FOR GEOMETRIC GRAPHS." International Journal of Computational Geometry & Applications 20, no. 04 (August 2010): 415–29. http://dx.doi.org/10.1142/s0218195910003360.

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In this paper we study proximity graph structures like Delaunay triangulations based on geometric graphs, i.e. graphs which are subgraphs of the complete geometric graph. Given an arbitrary geometric graph G, we define Voronoi diagrams, Delaunay triangulations, relative neighborhood graphs, Gabriel graphs which are related to the graph structure and then study their complexities when G is a general geometric graph or G is some special graph derived from the application area of wireless networks. Besides being of fundamental interest these structures have applications in topology control for wireless networks.

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Sun, Ze Yu, Qiao Jin, Lian Guang Jia, Qiang Wang, Yi Ma, and Chi Xu. "Finite Element Analysis of Seismic Responses of a Large-Cantilever Stadium Structure." Applied Mechanics and Materials 580-583 (July 2014): 1786–89. http://dx.doi.org/10.4028/www.scientific.net/amm.580-583.1786.

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In this paper, based on the Midas/gen platform, a three-dimensional finite element model (FEM) for a transfinite stadium with a large-span and large-cantilever roof , located in Shenyang, was used to study its potential responses to seismic activities. In the numerical analysis, an earthquake spectrum stipulated by the Chinese Seismic Code (GB50011-2010) was adopted to calculate the bidirectional horizontal displacements by the Complete Quadratic Combination (CQC) method on the basis of the response spectrum analysis. The computational results indicate that the maximum displacements in both of the two horizontal directions locate at the top of this structure, i.e. the transfinite part of the roof.

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Chorbadjiev, Lubomir, Jude Kendall, Joan Alexander, Viacheslav Zhygulin, Junyan Song, Michael Wigler, and Alexander Krasnitz. "Integrated Computational Pipeline for Single-Cell Genomic Profiling." JCO Clinical Cancer Informatics, no. 4 (September 2020): 464–71. http://dx.doi.org/10.1200/cci.19.00171.

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PURPOSE Copy-number profiling of multiple individual cells from sparse sequencing may be used to reveal a detailed picture of genomic heterogeneity and clonal organization in a tissue biopsy specimen. We sought to provide a comprehensive computational pipeline for single-cell genomics, to facilitate adoption of this molecular technology for basic and translational research. MATERIALS AND METHODS The pipeline comprises software tools programmed in Python and in R and depends on Bowtie, HISAT2, Matplotlib, and Qt. It is installed and used with Anaconda. RESULTS Here we describe a complete pipeline for sparse single-cell genomic data, encompassing all steps of single-nucleus DNA copy-number profiling, from raw sequence processing to clonal structure analysis and visualization. For the latter, a specialized graphical user interface termed the single-cell genome viewer (SCGV) is provided. With applications to cancer diagnostics in mind, the SCGV allows for zooming and linkage to the University of California at Santa Cruz Genome Browser from each of the multiple integrated views of single-cell copy-number profiles. The latter can be organized by clonal substructure or by any of the associated metadata such as anatomic location and histologic characterization. CONCLUSION The pipeline is available as open-source software for Linux and OS X. Its modular structure, extensive documentation, and ease of deployment using Anaconda facilitate its adoption by researchers and practitioners of single-cell genomics. With open-source availability and Massachusetts Institute of Technology licensing, it provides a basis for additional development by the cancer bioinformatics community.

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Cheng, Qian, Kexian Gong, Min Zhang, and Xiaoyan Liu. "An efficient wide-band signal detection and extraction method." MATEC Web of Conferences 336 (2021): 04011. http://dx.doi.org/10.1051/matecconf/202133604011.

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Aiming at the influence of time-varying and frequency-varying of noise on the signal detection performance in the short wave wide-band channel and the large amount of computation in the channelized receiver model of the traditional low pass filter bank, a cross-channel reconfigurable multi-phase high-efficiency channelization method based on morphological processing is proposed in this paper .Firstly, The wide-band signal is coarsely filtered by the multi-phase structure of the uniform filter bank which is determined by the protection interval between signals, and then the bandwidth and position of the signal are determined by improved morphological operation and threshold decision of the power spectrum. Finally, the sub-band signals across the channel are combined to complete the approximate reconstruction of the sub-signals. Compared with the computational complexity of traditional channelized receiver model, the results show that this method has lower computational complexity. The simulation results show that the method can achieve the approximate constant false alarm rate(CFAR) under the colored noise environment, and has higher detection capability under different signal-to-noise ratios(SNR).

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Solaichamy, R., and J. Karpagam. "Molecular Structure, Vibrational Spectra and Docking Studies of Abacavir by Density Functional Theory." International Letters of Chemistry, Physics and Astronomy 72 (January 2017): 9–27. http://dx.doi.org/10.18052/www.scipress.com/ilcpa.72.9.

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In this study, optimized geometry, spectroscopic (FT-IR, FT-Raman, UV) analysis, and electronic structure analysis of Abacavir were investigated by utilizing DFT/B3LYP with 6-31G(d,p) as a basis set. Complete vibrational assignments and correlation of the fundamental modes for the title compound were carried out. The calculated molecular geometry has been compared with available X-ray data of Abacavir. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The molecular stability and bond strength have been investigated by applying the Natural Bond Orbital (NBO) analysis. The computational molecular docking studies of title compound have been performed.

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Lv, Yunfei, Yongzhen Pei, and Rong Yuan. "Complete global analysis of a diffusive NPZ model with age structure in zooplankton." Nonlinear Analysis: Real World Applications 46 (April 2019): 274–97. http://dx.doi.org/10.1016/j.nonrwa.2018.09.016.

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Wan, Zhi-Qiang, Xiao-Zhe Wang, and Chao Yang. "Integrated aerodynamics/structure/stability optimization of large aircraft in conceptual design." Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering 232, no. 4 (January 11, 2017): 745–56. http://dx.doi.org/10.1177/0954410016687143.

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The multidisciplinary design optimization is suitable for modern large aircraft, and it has the potential in conceptual phase of aircraft design especially. An integrated optimization method considering the disciplines of aerodynamics, structure and stability for large aircraft design in conceptual phase is presented. The objective is the minimum stiffness of a beam-frame wing structure subject to aeroelasticity, aerodynamics, and stability constraints. The aeroelastic responses are computed by commercial software MSC. Nastran, and the cruise stability is evaluated by the linear small-disturbance equations. A viscous-inviscid iteration method, which is composed of a computational fluid dynamics tool solving the Euler equations and a viscous correction method, is used for computing the flow over the model. The method ensures effective and rapid computation. In this paper, a complete aircraft model is optimized, and all the responses are computed in the trim condition with a fixed maximum takeoff weight. Genetic algorithm is utilized for global optimizations, and the optimal jig shape, the elastic axis positions and the stiffness distribution can be attained adequately. The results show that the method has a value of application in engineering optimizations. For the satisfaction of the total drag and stability constraints, the structure weight usually needs a price to pay. The integrated optimization captures the tradeoff between aerodynamics, structure and stability, and the repeated design can be avoided.

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Heckendorn, Robert B., and Alden H. Wright. "Efficient Linkage Discovery by Limited Probing." Evolutionary Computation 12, no. 4 (December 2004): 517–45. http://dx.doi.org/10.1162/1063656043138914.

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This paper addresses the problem of discovering the structure of a fitness function from binary strings to the reals under the assumption of bounded epistasis. Two loci (string positions) are epistatically linked if the effect of changing the allele (value) at one locus depends on the allele at the other locus. Similarly, a group of loci are epistatically linked if the effect of changing the allele at one locus depends on the alleles at all other loci of the group. Under the assumption that the size of such groups of loci are bounded, and assuming that the function is given only as a “black box function”, this paper presents and analyzes a randomized algorithm that finds the complete epistatic structure of the function in the form of the Walsh coefficients of the function.

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ZAMBONELLI, FRANCO, NICHOLAS R. JENNINGS, and MICHAEL WOOLDRIDGE. "ORGANISATIONAL RULES AS AN ABSTRACTION FOR THE ANALYSIS AND DESIGN OF MULTI-AGENT SYSTEMS." International Journal of Software Engineering and Knowledge Engineering 11, no. 03 (June 2001): 303–28. http://dx.doi.org/10.1142/s0218194001000505.

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Multi-agent systems can very naturally be viewed as computational organisations. For this reason, we believe organisational abstractions offer a promising set of metaphors and models that can be exploited in the analysis and design of such systems. To this end, the concept of role models is increasingly being used to specify and design multi-agent systems. However, this is not the full picture. In this paper we introduce three additional organisational concepts — organisational rules, organisational structures, and organisational patterns — and discuss why we believe they are necessary for the complete specification of computational organisations. In particular, we focus on the concept of organisational rules and introduce a formalism, based on temporal logic, to specify them. This formalism is then used to drive the definition of the organisational structure and the identification of the organisational patterns. Finally, the paper sketches some guidelines for a methodology for agent-oriented systems based on our expanded set of organisational abstractions.

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Sabban, Sari, and Mikhail Markovsky. "RamaNet: Computational de novo helical protein backbone design using a long short-term memory generative neural network." F1000Research 9 (September 11, 2020): 298. http://dx.doi.org/10.12688/f1000research.22907.2.

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The ability to perform de novo protein design will allow researchers to expand the variety of available proteins. By designing synthetic structures computationally, they can utilise more structures than those available in the Protein Data Bank, design structures that are not found in nature, or direct the design of proteins to acquire a specific desired structure. While some researchers attempt to design proteins from first physical and thermodynamic principals, we decided to attempt to test whether it is possible to perform de novo helical protein design of just the backbone statistically using machine learning by building a model that uses a long short-term memory (LSTM) architecture. The LSTM model used only the φ and ψ angles of each residue from an augmented dataset of only helical protein structures. Though the network’s generated backbone structures were not perfect, they were idealised and evaluated post generation where the non-ideal structures were filtered out and the adequate structures kept. The results were successful in developing a logical, rigid, compact, helical protein backbone topology. This paper is a proof of concept that shows it is possible to generate a novel helical backbone topology using an LSTM neural network architecture using only the φ and ψ angles as features. The next step is to attempt to use these backbone topologies and sequence design them to form complete protein structures.

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Sabban, Sari, and Mikhail Markovsky. "RamaNet: Computational de novo helical protein backbone design using a long short-term memory generative neural network." F1000Research 9 (October 12, 2020): 298. http://dx.doi.org/10.12688/f1000research.22907.3.

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The ability to perform de novo protein design will allow researchers to expand the variety of available proteins. By designing synthetic structures computationally, they can utilise more structures than those available in the Protein Data Bank, design structures that are not found in nature, or direct the design of proteins to acquire a specific desired structure. While some researchers attempt to design proteins from first physical and thermodynamic principals, we decided to attempt to test whether it is possible to perform de novo helical protein design of just the backbone statistically using machine learning by building a model that uses a long short-term memory (LSTM) architecture. The LSTM model used only the φ and ψ angles of each residue from an augmented dataset of only helical protein structures. Though the network’s generated backbone structures were not perfect, they were idealised and evaluated post generation where the non-ideal structures were filtered out and the adequate structures kept. The results were successful in developing a logical, rigid, compact, helical protein backbone topology. This paper is a proof of concept that shows it is possible to generate a novel helical backbone topology using an LSTM neural network architecture using only the φ and ψ angles as features. The next step is to attempt to use these backbone topologies and sequence design them to form complete protein structures.

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Babu, M. Madan. "Computational approaches to study transcriptional regulation." Biochemical Society Transactions 36, no. 4 (July 22, 2008): 758–65. http://dx.doi.org/10.1042/bst0360758.

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In recent years, a number of technical and experimental advances have allowed us to obtain an unprecedented amount of information about living systems on a genomic scale. Although the complete genomes of many organisms are available due to the progress made in sequencing technology, the challenge to understand how the individual genes are regulated within the cell remains. Here, I provide an overview of current computational methods to investigate transcriptional regulation. I will first discuss how representing protein–DNA interactions as a network provides us with a conceptual framework to understand the organization of regulatory interactions in an organism. I will then describe methods to predict transcription factors and cis-regulatory elements using information such as sequence, structure and evolutionary conservation. Finally, I will discuss approaches to infer genome-scale transcriptional regulatory networks using experimentally characterized interactions from model organisms and by reverse-engineering regulatory interactions that makes use of gene expression data and genomewide location data. The methods summarized here can be exploited to discover previously uncharacterized transcriptional pathways in organisms whose genome sequence is known. In addition, such a framework and approach can be invaluable to investigate transcriptional regulation in complex microbial communities such as the human gut flora or populations of emerging pathogens. Apart from these medical applications, the concepts and methods discussed can be used to understand the combinatorial logic of transcriptional regulation and can be exploited in biotechnological applications, such as in synthetic biology experiments aimed at engineering regulatory circuits for various purposes.

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Ferentz, Ann E., and Gerhard Wagner. "NMR spectroscopy: a multifaceted approach to macromolecular structure." Quarterly Reviews of Biophysics 33, no. 1 (February 2000): 29–65. http://dx.doi.org/10.1017/s0033583500003589.

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1. Introduction 292. Landmarks in NMR of macromolecules 322.1 Protein structures and methods development 322.1.1 Sequential assignment method 322.1.2 Triple-resonance experiments 342.1.3 Structures of large proteins 362.2 Protein–nucleic acid complexes 372.3 RNA structures 382.4 Membrane-bound systems 393. NMR spectroscopy today 403.1 State-of-the-art structure determination 413.2 New methods 443.2.1 Residual dipolar couplings 443.2.2 Direct detection of hydrogen bonds 443.2.3 Spin labeling 453.2.4 Segmental labeling 463.3 Protein complexes 473.4 Mobility studies 503.5 Determination of time-dependent structures 523.6 Drug discovery 534. The future of NMR 544.1 The ease of structure determination 544.2 The ease of making recombinant protein 554.3 Post-translationally modified proteins 554.4 Approaches to large and/or membrane-bound proteins 564.5 NMR in structural genomics 564.6 Synergy of NMR and crystallography in protein structure determination 565. Conclusion 576. Acknowledgements 577. References 57Since the publication of the first complete solution structure of a protein in 1985 (Williamson et al. 1985), tremendous technological advances have brought nuclear magnetic resonance spectroscopy to the forefront of structural biology. Innovations in magnet design, electronics, pulse sequences, data analysis, and computational methods have combined to make NMR an extremely powerful technique for studying biological macromolecules at atomic resolution (Clore & Gronenborn, 1998). Most recently, new labeling and pulse techniques have been developed that push the fundamental line-width limit for resolution in NMR spectroscopy, making it possible to obtain high-field spectra with better resolution than ever before (Dötsch & Wagner, 1998). These methods are facilitating the study of systems of ever-increasing complexity and molecular weight.

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Journal articles on the topic 'Complete computational structure'

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