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Entropy, Volume 14, Issue 3 (March 2012) – 11 articles , Pages 390-598

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1541 KiB  
Review
Application of Solution NMR Spectroscopy to Study Protein Dynamics
by Christoph Göbl and Nico Tjandra
Entropy 2012, 14(3), 581-598; https://doi.org/10.3390/e14030581 - 22 Mar 2012
Cited by 18 | Viewed by 11372
Abstract
Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to [...] Read more.
Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR) spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes. Full article
(This article belongs to the Special Issue Loop Entropy)
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174 KiB  
Article
Benefit-Cost Analysis of Security Systems for Multiple Protected Assets Based on Information Entropy
by Jingjing Dai, Ruimin Hu, Jun Chen and Qing Cai
Entropy 2012, 14(3), 571-580; https://doi.org/10.3390/e14030571 - 14 Mar 2012
Cited by 8 | Viewed by 6817
Abstract
This article proposes a quantitative risk assessment for security systems which have multiple protected assets and a risk-based benefit-cost analysis for decision makers. The proposed methodology consists of five phases: identification of assets, security unit and intrusion path, security unit effectiveness estimation, intrusion [...] Read more.
This article proposes a quantitative risk assessment for security systems which have multiple protected assets and a risk-based benefit-cost analysis for decision makers. The proposed methodology consists of five phases: identification of assets, security unit and intrusion path, security unit effectiveness estimation, intrusion path effectiveness estimation, security system risk assessment and benefit-cost estimation. Key innovations in this methodology include its use of effectiveness entropy to measure the degree of uncertainty of a security system to complete a protection task, and the fact it measures risk like information theory measures the amount of information. A notional example is provided to demonstrate an application of the proposed methodology. Full article
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133 KiB  
Article
Entropy and the Complexity of Graphs Revisited
by Abbe Mowshowitz and Matthias Dehmer
Entropy 2012, 14(3), 559-570; https://doi.org/10.3390/e14030559 - 14 Mar 2012
Cited by 157 | Viewed by 11705
Abstract
This paper presents a taxonomy and overview of approaches to the measurement of graph and network complexity. The taxonomy distinguishes between deterministic (e.g., Kolmogorov complexity) and probabilistic approaches with a view to placing entropy-based probabilistic measurement in context. Entropy-based measurement is the main [...] Read more.
This paper presents a taxonomy and overview of approaches to the measurement of graph and network complexity. The taxonomy distinguishes between deterministic (e.g., Kolmogorov complexity) and probabilistic approaches with a view to placing entropy-based probabilistic measurement in context. Entropy-based measurement is the main focus of the paper. Relationships between the different entropy functions used to measure complexity are examined; and intrinsic (e.g., classical measures) and extrinsic (e.g., Körner entropy) variants of entropy-based models are discussed in some detail. Full article
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323 KiB  
Article
Curvature Entropy for Curved Profile Generation
by Yoshiki Ujiie, Takeo Kato, Koichiro Sato and Yoshiyuki Matsuoka
Entropy 2012, 14(3), 533-558; https://doi.org/10.3390/e14030533 - 9 Mar 2012
Cited by 19 | Viewed by 7498
Abstract
In a curved surface design, the overall shape features that emerge from combinations of shape elements are important. However, controlling the features of the overall shape in curved profiles is difficult using conventional microscopic shape information such as dimension. Herein two types of [...] Read more.
In a curved surface design, the overall shape features that emerge from combinations of shape elements are important. However, controlling the features of the overall shape in curved profiles is difficult using conventional microscopic shape information such as dimension. Herein two types of macroscopic shape information, curvature entropy and quadrature curvature entropy, quantitatively represent the features of the overall shape. The curvature entropy is calculated by the curvature distribution, and represents the complexity of a shape (one of the overall shape features). The quadrature curvature entropy is an improvement of the curvature entropy by introducing a Markov process to evaluate the continuity of a curvature and to approximate human cognition of the shape. Additionally, a shape generation method using a genetic algorithm as a calculator and the entropy as a shape generation index is presented. Finally, the applicability of the proposed method is demonstrated using the side view of an automobile as a design example. Full article
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260 KiB  
Article
Energy and Exergy Analysis for Improving the Energy Performance of Air-Cooled Liquid Chillers by Different Condensing-Coil Configurations
by Wu-Chieh Wu, Tzong-Shing Lee and Chich-Hsiang Chang
Entropy 2012, 14(3), 517-532; https://doi.org/10.3390/e14030517 - 8 Mar 2012
Cited by 4 | Viewed by 7834
Abstract
This study constructed a parameter analysis for improving the energy performance of air-cooled water chillers by altering the angle configuration of the condenser coils. The mathematical models for energy and exergy analyses of the individual components and overall system of air-cooled water chillers [...] Read more.
This study constructed a parameter analysis for improving the energy performance of air-cooled water chillers by altering the angle configuration of the condenser coils. The mathematical models for energy and exergy analyses of the individual components and overall system of air-cooled water chillers are presented. This study investigated the potential enhancement of performance efficiency in air-cooled chillers and the energy conversion efficiency of each component, in order to determine how the angle configuration of condenser coils influences chiller performance. This study found that the overall performance of an air-cooled chiller could be improved by approximately 3.4%, and the total irreversibility could be reduced by approximately 2.7%. With each 1% increase in average wind speed over the condenser coils, the overall performance of an air‑cooled chiller was found to be enhanced by approximately 0.43%, and its total irreversibility was reduced by approximately 0.35%. The results of this study can be effectively applied to air-cooled condenser units, and can provide an important basis of reference for developing and enhancing the energy efficiency of air-cooled chillers. Full article
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126 KiB  
Article
Minimum Error Entropy Filter for Fault Detection of Networked Control Systems
by Jianhua Zhang, Lilong Du, Mifeng Ren and Guolian Hou
Entropy 2012, 14(3), 505-516; https://doi.org/10.3390/e14030505 - 6 Mar 2012
Cited by 10 | Viewed by 6365
Abstract
In this paper, fault detection of networked control systems with random delays, packet dropout and noises is studied. The filter is designed using a minimum error entropy criterion. The residual generated by the filter is then evaluated to detect faults in networked control [...] Read more.
In this paper, fault detection of networked control systems with random delays, packet dropout and noises is studied. The filter is designed using a minimum error entropy criterion. The residual generated by the filter is then evaluated to detect faults in networked control systems. An illustrative networked control system is used to verify the effectiveness of the proposed approach. Full article
(This article belongs to the Special Issue Information Theory Applied to Communications and Networking)
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161 KiB  
Article
The Optimal Evaporation Temperature of Subcritical ORC Based on Second Law Efficiency for Waste Heat Recovery
by Chao Liu, Chao He, Hong Gao, Xiaoxiao Xu and Jinliang Xu
Entropy 2012, 14(3), 491-504; https://doi.org/10.3390/e14030491 - 6 Mar 2012
Cited by 47 | Viewed by 8373
Abstract
The subcritical Organic Rankine Cycle (ORC) with 28 working fluids for waste heat recovery is discussed in this paper. The effects of the temperature of the waste heat, the critical temperature of working fluids and the pinch temperature difference in the evaporator on [...] Read more.
The subcritical Organic Rankine Cycle (ORC) with 28 working fluids for waste heat recovery is discussed in this paper. The effects of the temperature of the waste heat, the critical temperature of working fluids and the pinch temperature difference in the evaporator on the optimal evaporation temperature (OET) of the ORC have been investigated. The second law efficiency of the system is regarded as the objective function and the evaporation temperature is optimized by using the quadratic approximations method. The results show that the OET will appear for the temperature ranges investigated when the critical temperatures of working fluids are lower than the waste heat temperatures by 18 ± 5 K under the pinch temperature difference of 5 K in the evaporator. Additionally, the ORC always exhibits the OET when the pinch temperature difference in the evaporator is raised under the fixed waste heat temperature. The maximum second law efficiency will decrease with the increase of pinch temperature difference in the evaporator. Full article
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119 KiB  
Article
Interval Entropy and Informative Distance
by Fakhroddin Misagh and Gholamhossein Yari
Entropy 2012, 14(3), 480-490; https://doi.org/10.3390/e14030480 - 2 Mar 2012
Cited by 35 | Viewed by 7233
Abstract
The Shannon interval entropy function as a useful dynamic measure of uncertainty for two sided truncated random variables has been proposed in the literature of reliability. In this paper, we show that interval entropy can uniquely determine the distribution function. Furthermore, we propose [...] Read more.
The Shannon interval entropy function as a useful dynamic measure of uncertainty for two sided truncated random variables has been proposed in the literature of reliability. In this paper, we show that interval entropy can uniquely determine the distribution function. Furthermore, we propose a measure of discrepancy between two lifetime distributions at the interval of time in base of Kullback-Leibler discrimination information. We study various properties of this measure, including its connection with residual and past measures of discrepancy and interval entropy, and we obtain its upper and lower bounds. Full article
(This article belongs to the Special Issue Concepts of Entropy and Their Applications)
221 KiB  
Article
The Mathematical Structure of Information Bottleneck Methods
by Tomáš Gedeon, Albert E. Parker and Alexander G. Dimitrov
Entropy 2012, 14(3), 456-479; https://doi.org/10.3390/e14030456 - 1 Mar 2012
Cited by 17 | Viewed by 7462
Abstract
Information Bottleneck-based methods use mutual information as a distortion function in order to extract relevant details about the structure of a complex system by compression. One of the approaches used to generate optimal compressed representations is by annealing a parameter. In this manuscript [...] Read more.
Information Bottleneck-based methods use mutual information as a distortion function in order to extract relevant details about the structure of a complex system by compression. One of the approaches used to generate optimal compressed representations is by annealing a parameter. In this manuscript we present a common framework for the study of annealing in information distortion problems. We identify features that should be common to any annealing optimization problem. The main mathematical tools that we use come from the analysis of dynamical systems in the presence of symmetry (equivariant bifurcation theory). Through the compression problem, we make connections to the world of combinatorial optimization and pattern recognition. The two approaches use very different vocabularies and consider different problems to be “interesting”. We provide an initial link, through the Normalized Cut Problem, where the two disciplines can exchange tools and ideas. Full article
(This article belongs to the Special Issue The Information Bottleneck Method)
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356 KiB  
Article
Temporal Asymmetry, Entropic Irreversibility, and Finite-Time Thermodynamics: From Parmenides–Einstein Time-Reversal Symmetry to the Heraclitan Entropic Arrow of Time
by Wassim M. Haddad
Entropy 2012, 14(3), 407-455; https://doi.org/10.3390/e14030407 - 28 Feb 2012
Cited by 12 | Viewed by 6969
Abstract
In this paper, we combine the two universalisms of thermodynamics and dynamical systems theory to develop a dynamical system formalism for classical thermodynamics. Specifically, using a compartmental dynamical system energy flow model we develop a state-space dynamical system model that captures the key [...] Read more.
In this paper, we combine the two universalisms of thermodynamics and dynamical systems theory to develop a dynamical system formalism for classical thermodynamics. Specifically, using a compartmental dynamical system energy flow model we develop a state-space dynamical system model that captures the key aspects of thermodynamics, including its fundamental laws. In addition, we establish the existence of a unique, continuously differentiable global entropy function for our dynamical system model, and using Lyapunov stability theory we show that the proposed thermodynamic model has finite-time convergent trajectories to Lyapunov stable equilibria determined by the system initial energies. Finally, using the system entropy, we establish the absence of Poincaré recurrence for our thermodynamic model and develop clear and rigorous connections between irreversibility, the second law of thermodynamics, and the entropic arrow of time. Full article
(This article belongs to the Special Issue Arrow of Time)
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448 KiB  
Article
Bumps on the Road to Here (from Eternity)
by Eric Winsberg
Entropy 2012, 14(3), 390-406; https://doi.org/10.3390/e14030390 - 23 Feb 2012
Cited by 9 | Viewed by 11130
Abstract
In his recent book, From Eternity to Here, and in other more technical papers, Sean Carroll (partly in collaboration with Jennifer Chen) has put forward an intriguing new way to think about the origin of the Universe. His approach, in a nutshell, [...] Read more.
In his recent book, From Eternity to Here, and in other more technical papers, Sean Carroll (partly in collaboration with Jennifer Chen) has put forward an intriguing new way to think about the origin of the Universe. His approach, in a nutshell, is to raise certain worries about a standard Boltzmannian picture of statistical mechanics, and to present certain commitments that he thinks we ought to hold—commitments that the standard picture doesn’t share. He then proposes a cosmological model—one that purports to give us insight into what sort of process brought about the “initial state” of the universe—that can uniquely accommodate those commitments. The conclusion of Carroll’s argument is that statistical mechanical reasoning provides grounds for provisionally accepting that cosmological model. My goal in this paper is to reconstruct and critically assess this proposal. I argue that “statistical cosmology” requires a careful balance of philosophical intuitions and commitments against technical, scientific considerations; how much stock we ought to place in these intuitions and commitments should depend on where they lead us—those that lead us astray scientifically might well be in need of philosophical re‑examination. Full article
(This article belongs to the Special Issue Arrow of Time)
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