scholarly journals Ten things I `hate' about refinement

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Pietro Roversi ◽  
Dale E. Tronrud
Keyword(s):  
Experimental Data ◽  
Chemical Structure ◽  
Structural Model ◽  
Optimization Problems ◽  
First Century ◽  
Complex Relationship ◽  
Unfinished Business ◽  
Modern Computer ◽  
Complex Optimization ◽  
Computer Resources

Macromolecular refinement is an optimization process that aims to produce the most likely macromolecular structural model in the light of experimental data. As such, macromolecular refinement is one of the most complex optimization problems in wide use. Macromolecular refinement programs have to deal with the complex relationship between the parameters of the atomic model and the experimental data, as well as a large number of types of prior knowledge about chemical structure. This paper draws attention to areas of unfinished business in the field of macromolecular refinement. In it, we describe ten refinement topics that we think deserve attention and discuss directions leading to macromolecular refinement software that would make the best use of modern computer resources to meet the needs of structural biologists of the twenty-first century.

Dimer Reconstruction at Metal-Silicide/Silicon Interfaces: A First-Principles Study

1999 ◽  
Vol 564 ◽  
Author(s):  
B. D. Yu ◽  
Y. Miyamoto ◽  
O. Sugino ◽  
A. Sakai ◽  
T. Sasaki ◽  
...  
Keyword(s):  
Experimental Data ◽  
Total Energy ◽  
Surface Reconstruction ◽  
First Principles ◽  
Chemical Structure ◽  
Schottky Barrier Height ◽  
Structural Model ◽  
Metal Silicide ◽  
Interface Model ◽  
Interface Structures

AbstractBy employing first-principles total-energy calculations we studied the atomic and chemical structure of NiSi2/Si(001) and CoSi2/Si(001) interfaces that are of great importance in understanding electronic properties, such as the Schottky-barrier height, of metal-silicide/silicon junctions. We found a new structural model that is more stable than previously proposed models of interface structures and well explains existing experimental data. The new interface model consists of sevenfold-coordinated interfacial metals and a 2×1 periodic array of interfacial Si dimers, similar to the Si(001) 2×1 surface reconstruction, reducing the number of dangling bonds.

scholarly journals Search Patterns Based on Trajectories Extracted from the Response of Second-Order Systems

2021 ◽  
Vol 11 (8) ◽  
pp. 3430
Author(s):  
Erik Cuevas ◽  
Héctor Becerra ◽  
Héctor Escobar ◽  
Alberto Luque-Chang ◽  
Marco Pérez ◽  
...  
Keyword(s):  
Convergence Rates ◽  
Optimization Problems ◽  
Search Space ◽  
Second Order ◽  
Order System ◽  
Search Patterns ◽  
Multiple Behaviors ◽  
Complex Optimization ◽  
Second Order Systems ◽  
Order Algorithm

Recently, several new metaheuristic schemes have been introduced in the literature. Although all these approaches consider very different phenomena as metaphors, the search patterns used to explore the search space are very similar. On the other hand, second-order systems are models that present different temporal behaviors depending on the value of their parameters. Such temporal behaviors can be conceived as search patterns with multiple behaviors and simple configurations. In this paper, a set of new search patterns are introduced to explore the search space efficiently. They emulate the response of a second-order system. The proposed set of search patterns have been integrated as a complete search strategy, called Second-Order Algorithm (SOA), to obtain the global solution of complex optimization problems. To analyze the performance of the proposed scheme, it has been compared in a set of representative optimization problems, including multimodal, unimodal, and hybrid benchmark formulations. Numerical results demonstrate that the proposed SOA method exhibits remarkable performance in terms of accuracy and high convergence rates.

scholarly journals Chunking and cooperation in particle swarm optimization for feature selection

2021 ◽  
Author(s):  
Malek Sarhani ◽  
Stefan Voß
Keyword(s):  
Feature Selection ◽  
Particle Swarm Optimization ◽  
Cooperative Learning ◽  
Optimization Problems ◽  
Practical Importance ◽  
Particle Swarm ◽  
Large Datasets ◽  
Social Phenomena ◽  
Swarm Optimization ◽  
Complex Optimization

AbstractBio-inspired optimization aims at adapting observed natural behavioral patterns and social phenomena towards efficiently solving complex optimization problems, and is nowadays gaining much attention. However, researchers recently highlighted an inconsistency between the need in the field and the actual trend. Indeed, while nowadays it is important to design innovative contributions, an actual trend in bio-inspired optimization is to re-iterate the existing knowledge in a different form. The aim of this paper is to fill this gap. More precisely, we start first by highlighting new examples for this problem by considering and describing the concepts of chunking and cooperative learning. Second, by considering particle swarm optimization (PSO), we present a novel bridge between these two notions adapted to the problem of feature selection. In the experiments, we investigate the practical importance of our approach while exploring both its strength and limitations. The results indicate that the approach is mainly suitable for large datasets, and that further research is needed to improve the computational efficiency of the approach and to ensure the independence of the sub-problems defined using chunking.

scholarly journals A Shuffle-Based Artificial Bee Colony Algorithm for Solving Integer Programming and Minimax Problems

Mathematics ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1211
Author(s):  
Ivona Brajević
Keyword(s):  
Integer Programming ◽  
Artificial Bee Colony ◽  
Optimization Problems ◽  
Minimax Problems ◽  
Abc Algorithm ◽  
Bee Colony ◽  
Effective Performance ◽  
Complex Optimization ◽  
Overall Performance ◽  
Integer Programming Problems

The artificial bee colony (ABC) algorithm is a prominent swarm intelligence technique due to its simple structure and effective performance. However, the ABC algorithm has a slow convergence rate when it is used to solve complex optimization problems since its solution search equation is more of an exploration than exploitation operator. This paper presents an improved ABC algorithm for solving integer programming and minimax problems. The proposed approach employs a modified ABC search operator, which exploits the useful information of the current best solution in the onlooker phase with the intention of improving its exploitation tendency. Furthermore, the shuffle mutation operator is applied to the created solutions in both bee phases to help the search achieve a better balance between the global exploration and local exploitation abilities and to provide a valuable convergence speed. The experimental results, obtained by testing on seven integer programming problems and ten minimax problems, show that the overall performance of the proposed approach is superior to the ABC. Additionally, it obtains competitive results compared with other state-of-the-art algorithms.

Benchmark of a Novel Aero-Elastic Simulation Code for Small Scale VAWT Analysis

2018 ◽  
Vol 141 (4) ◽  
Author(s):  
David Marten ◽  
Matthew Lennie ◽  
George Pechlivanoglou ◽  
Christian Oliver Paschereit ◽  
Alessandro Bianchini ◽  
...  
Keyword(s):  
Experimental Data ◽  
Wind Turbine ◽  
Open Source ◽  
Structural Model ◽  
Element Model ◽  
Small Scale ◽  
Elastic Model ◽  
Element Analysis ◽  
Simulation Code ◽  
Highly Nonlinear

After almost 20 years of absence from research agendas, interest in the vertical axis wind turbine (VAWT) technology is presently increasing again, after the research stalled in the mid 90's in favor of horizontal axis wind turbines (HAWTs). However, due to the lack of research in past years, there are a significantly lower number of design and certification tools available, many of which are underdeveloped if compared to the corresponding tools for HAWTs. To partially fulfill this gap, a structural finite element analysis (FEA) model, based on the Open Source multiphysics library PROJECT::CHRONO, was recently integrated with the lifting line free vortex wake (LLFVW) method inside the Open Source wind turbine simulation code QBlade and validated against numerical and experimental data of the SANDIA 34 m rotor. In this work, some details about the newly implemented nonlinear structural model and its coupling to the aerodynamic solver are first given. Then, in a continuous effort to assess its accuracy, the code capabilities were here tested on a small-scale, fast-spinning (up to 450 rpm) VAWT. The study turbine is a helix shaped, 1 kW Darrieus turbine, for which other numerical analyses were available from a previous study, including the results coming from both a one-dimensional beam element model and a more sophisticated shell element model. The resulting data represented an excellent basis for comparison and validation of the new aero-elastic coupling in QBlade. Based on the structural and aerodynamic data of the study turbine, an aero-elastic model was then constructed. A purely aerodynamic comparison to experimental data and a blade element momentum (BEM) simulation represented the benchmark for QBlade aerodynamic performance. Then, a purely structural analysis was carried out and compared to the numerical results from the former. After the code validation, an aero-elastically coupled simulation of a rotor self-start has been performed to demonstrate the capabilities of the newly developed model to predict the highly nonlinear transient aerodynamic and structural rotor response.

scholarly journals Подход к решению задачи оптимизации логистики агрохолдинга

2013 ◽  
pp. 139-144
Author(s):  
Е. В. Скакалина
Keyword(s):  
Information Technology ◽  
Discrete Optimization ◽  
Optimization Problems ◽  
Implementation Process ◽  
Optimal Solutions ◽  
New Class ◽  
Modern Computer ◽  
Foreign Countries ◽  
Intensive Development ◽  
Discrete Optimization Problems

У роботі наведено короткий аналіз використання інформаційних технологій в аграрному напрямі. Вказу-ється на можливість удосконалення управління проце-сом реалізації логістики великих агрохолдингів за раху-нок використання ефективного методу побудови оп-тимальних рішень для узагальнень задачі про призна-чення. Представлений новий клас дискретних оптимі-заційних задач. Звертається увага на інтенсивний роз-виток логістики у зарубіжних країнах на основі викори-стання сучасних комп'ютерних технологій. The paper presents a brief analysis of the use of information technology in the agricultural area. The possibility of improvement of management of logistics implementation process of large agricultural holdings through the use of an effective method of optimal solutions constructing for generalizations of the assignment problem is shown. A new class of discrete optimization problems is presented. The attention is drawn to the intensive development of logistics in foreign countries on the basis of use of modern computer technologies.

scholarly journals A Survey on Dragonfly Algorithm and its Applications in Engineering

2020 ◽  
Author(s):  
Chnoor M. Rahman ◽  
Tarik A. Rashid
Keyword(s):  
Review Paper ◽  
Optimization Problems ◽  
Optimization Techniques ◽  
Superior Performance ◽  
Test Functions ◽  
Dragonfly Algorithm ◽  
Engineering Problems ◽  
Complex Optimization ◽  
Metaheuristic Techniques ◽  
Benchmark Test Functions

<p></p><p></p><p>Dragonfly algorithm developed in 2016. It is one of the algorithms used by the researchers to optimize an extensive series of uses and applications in various areas. At times, it offers superior performance compared to the most well-known optimization techniques. However, this algorithm faces several difficulties when it is utilized to enhance complex optimization problems. This work addressed the robustness of the method to solve real-world optimization issues, and its deficiency to improve complex optimization problems. This review paper shows a comprehensive investigation of the dragonfly algorithm in the engineering area. First, an overview of the algorithm is discussed. Besides, we also examine the modifications of the algorithm. The merged forms of this algorithm with different techniques and the modifications that have been done to make the algorithm perform better are addressed. Additionally, a survey on applications in the engineering area that used the dragonfly algorithm is offered. A comparison is made between the algorithm and other metaheuristic techniques to show its ability to enhance various problems. The outcomes of the algorithm from the works that utilized the dragonfly algorithm previously and the outcomes of the benchmark test functions proved that in comparison with some techniques, the dragonfly algorithm owns an excellent performance, especially for small to intermediate applications. Moreover, the congestion facts of the technique and some future works are presented. The authors conducted this research to help other researchers who want to study the algorithm and utilize it to optimize engineering problems.</p><br><p></p><p></p>

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