Entropy

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Open AccessArticle

Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins

by Mihail Mihailescu and Hagai Meirovitch

Entropy 2010, 12(8), 1946-1974; https://doi.org/10.3390/e12081946 - 25 Aug 2010

Cited by 3 | Viewed by 7981

A mobile loop changes its conformation from “open” (free enzyme) to “closed” upon ligand binding. The difference in the Helmholtz free energy, ΔF_loop between these states sheds light on the mechanism of binding. With our “hypothetical scanning molecular dynamics” (HSMD-TI) method [...] Read more.

A mobile loop changes its conformation from “open” (free enzyme) to “closed” upon ligand binding. The difference in the Helmholtz free energy, ΔF_loop between these states sheds light on the mechanism of binding. With our “hypothetical scanning molecular dynamics” (HSMD-TI) method ΔF_loop= F_free − F_boundwhere F_free and F_boundare calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI) procedure. In previous work the free and bound loop structures were both attached to the same “template” which was “cut” from the crystal structure of the free protein. Our results for loop 287−290 of AcetylCholineEsterase agree with the experiment, ΔF_loop~ −4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., N_water = 140 − 180 waters in a sphere of a 18 Å radius. Here we calculate ΔF_loop for the more realistic case, where two templates are “cut” from the crystal structures, 2dfp.pdb (bound) and 2ace.pdb (free), where N_water = 40 − 160; this requires adding a computationally more demanding (second) TI procedure. While the results for N_water≤ 140 are computationally sound, ΔF_loop is always positive (18 ± 2 kcal/mol for N_water = 140). These (disagreeing) results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å² for 2ace). While this conformational uncertainty is an inherent difficulty, the (unstable) results for N_water = 160 suggest that it might be alleviated by applying different (initial) structural optimizations to each template. Full article

(This article belongs to the Special Issue Configurational Entropy)

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198 KiB

Open AccessArticle

In Defense of Gibbs and the Traditional Definition of the Entropy of Distinguishable Particles

by John F. Nagle

Entropy 2010, 12(8), 1936-1945; https://doi.org/10.3390/e12081936 - 24 Aug 2010

Cited by 10 | Viewed by 8377

Abstract

The traditional Gibbs’ calculation of the entropy of distinguishable classical particles that leads to Gibbs Paradox has been criticized recently. This criticism, if valid, would require a substantially different definition of entropy in general. However, the traditional definition of entropy works quite well [...] Read more.

The traditional Gibbs’ calculation of the entropy of distinguishable classical particles that leads to Gibbs Paradox has been criticized recently. This criticism, if valid, would require a substantially different definition of entropy in general. However, the traditional definition of entropy works quite well in situations where the distinguishability of classical particles is taken seriously while a suggested replacement definition fails. Full article

(This article belongs to the Special Issue Gibbs Paradox and Its Resolutions)

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373 KiB

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A Statistical Thermodynamical Interpretation of Metabolism

by Friedrich Srienc and Pornkamol Unrean

Entropy 2010, 12(8), 1921-1935; https://doi.org/10.3390/e12081921 - 17 Aug 2010

Cited by 20 | Viewed by 9153

Abstract

The metabolic network of a cell can be decomposed into discrete elementary modes that contribute, each with a certain probability, to the overall flux through the metabolism. These modes are cell function supporting, fundamental pathways that represent permissible ‘quantum’ states of the metabolism. [...] Read more.

The metabolic network of a cell can be decomposed into discrete elementary modes that contribute, each with a certain probability, to the overall flux through the metabolism. These modes are cell function supporting, fundamental pathways that represent permissible ‘quantum’ states of the metabolism. For the case that cellular regulatory mechanisms for pathway fluxes evolved in an unbiased way, we demonstrate theoretically that the usage probabilities of individual elementary modes are distributed according to Boltzmann’s distribution law such that the rate of entropy production is maximized. Such distribution can be observed experimentally in highly evolved metabolic networks. Therefore, cell function has a natural tendency to operate at a maximum rate of entropy generation using preferentially efficient pathways with small reaction entropies. Ultimately, evolution of metabolic networks appears to be driven by forces that can be quantified by the distance of the current metabolic state from the state of maximum entropy generation that represents the unbiased, most probable selection of fundamental pathway choices. Full article

(This article belongs to the Special Issue Advances in Thermodynamics)

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277 KiB

Open AccessArticle

Cybersemiotics: An Evolutionary World View Going Beyond Entropy and Information into the Question of Meaning

by Søren Brier

Entropy 2010, 12(8), 1902-1920; https://doi.org/10.3390/e12081902 - 9 Aug 2010

Cited by 27 | Viewed by 12238

Abstract

What makes Cybersemiotics different from other approaches attempting to produce a transdisciplinary theory of information, cognition and communication is its absolute naturalism, which forces us to view life, consciousness and cultural meaning all as a part of nature and evolution. It thus opposes [...] Read more.

What makes Cybersemiotics different from other approaches attempting to produce a transdisciplinary theory of information, cognition and communication is its absolute naturalism, which forces us to view life, consciousness and cultural meaning all as a part of nature and evolution. It thus opposes a number of orthodoxies: 1. The physico-chemical scientific paradigm based on third person objective empirical knowledge and mathematical theory, but with no conceptions of experiental life, meaning and first person embodied consciousness and therefore meaningful linguistic intersubjectivity; 2. The biological and natural historical science approach understood as the combination of genetic evolutionary theory with an ecological and thermodynamic view based on the evolution of experiental living systems as the ground fact and engaged in a search for empirical truth, yet doing so without a theory of meaning and first person embodied consciousness and thereby linguistic meaningful intersubjectivity; 3. The linguistic-cultural-social structuralist constructivism that sees all knowledge as constructions of meaning produced by the intersubjective web of language, cultural mentality and power, but with no concept of empirical truth, life, evolution, ecology and a very weak concept of subjective embodied first person consciousness even while taking conscious intersubjective communication and knowledge processes as the basic fact to study (the linguistic turn); 4. Any approach which takes the qualitative distinction between subject and object as the ground fact, on which all meaningful knowledge is based, considering all result of the sciences including linguistics and embodiment of consciousness as secondary knowledge, as opposed to a phenomenological (Husserl) or actually phaneroscopic (Peirce) first person point of view considering conscious meaningful experiences in advance of the subject/object distinction. The phaneroscopic semiotics includes an intersubjective base as Peirce considers all knowledge as intersubjectively produced through signs and view emotions and qualia as Firstness. The integrative transdisciplinary synthesis of Cybersemiotics starts by accepting two major, but not fully explanatory, and very different transdisciplinary paradigms: 1. The second order cybernetic and autopoietic approach united in Luhmann’s triple autopoietic system theory of social communication; 2. The Peircean phaneroscopic, triadic, pragmaticistic, evolutionary, semiotic approach to meaning, which has led to modern biosemiotics, based in a phenomenological intersubjective world of partly self-organizing triadic sign processes in an experiental meaningful world. The two are integrated by inserting the modern development of information theory and self-organizing emergent chemico-biological phenomena as an aspect of a general semiotic evolution in the Peircean framework. This creates the Cybersemiotic framework, where evolutionary experiental and intersubjective sign processes become the ground reality, on which our conceptions of ourselves, action, meaning and the word are built. None of the results from exact science, biology, humanities or social sciences are considered more fundamental than the others. They contribute on an equal footing to our intersubjective semiotics knowing process of ourselves and the world Full article

(This article belongs to the Special Issue Cybersemiotics—Integration of the informational and semiotic paradigms of cognition and communication)

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278 KiB

Open AccessArticle

Reflections on Friction in Quantum Mechanics

by Yair Rezek

Entropy 2010, 12(8), 1885-1901; https://doi.org/10.3390/e12081885 - 9 Aug 2010

Cited by 40 | Viewed by 8757

Abstract

Distinctly quantum friction effects of three types are surveyed: internalfriction, measurement-induced friction, and quantum-fluctuation-induced friction. We demonstrate that external driving will lead to quantum internal friction, and critique the measurement-based interpretation of friction. We conclude that in general systems will experience internal and [...] Read more.

Distinctly quantum friction effects of three types are surveyed: internalfriction, measurement-induced friction, and quantum-fluctuation-induced friction. We demonstrate that external driving will lead to quantum internal friction, and critique the measurement-based interpretation of friction. We conclude that in general systems will experience internal and external quantum friction over and beyond the classical frictional contributions. Full article

(This article belongs to the Special Issue Entropy and Friction Volume 2)

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276 KiB

Open AccessArticle

Second Law Analysis of Viscoelastic Fluid over a Stretching Sheet Subject to a Transverse Magnetic Field with Heat and Mass Transfer

by Soraya Aïboud and Salah Saouli

Entropy 2010, 12(8), 1867-1884; https://doi.org/10.3390/e12081867 - 28 Jul 2010

Cited by 40 | Viewed by 7002

Abstract

This paper concerns the second law analysis of a viscoelastic fluid over a stretching sheet subject to a transverse magnetic field with heat and mass transfer. The velocity, temperature and concentration profiles are obtained analytically using Kummer’s functions. The effects of the magnetic [...] Read more.

This paper concerns the second law analysis of a viscoelastic fluid over a stretching sheet subject to a transverse magnetic field with heat and mass transfer. The velocity, temperature and concentration profiles are obtained analytically using Kummer’s functions. The effects of the magnetic and viscoelastic parameters on both the longitudianl and the transverse velocities are investigated. The influence of Prandt number, the magnetic parameter and the heat source/sink parameter on the temperature is analysed. The concentration and its variations with the Schmidt number and the magnetic parameter is presented as well. The velocity, the temperature and the concentration profiles are used to compute the entropy generation number. This number is graphed and studied as function of the magnetic parameter, the Prandtl number, The Schmidt number, the Reynolds number, the dimensionless group, the Hartmann number, the ratio of the dimensionless concentration difference to the dimensionless temperature difference and the constant parameter. Full article

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185 KiB

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Entropy Generation Minima in Different Configurations of the Branching of a Fluid-Carrying Pipe in Laminar Isothermal Flow

by Enrico Sciubba

Entropy 2010, 12(8), 1855-1866; https://doi.org/10.3390/e12081855 - 26 Jul 2010

Cited by 22 | Viewed by 8046

Abstract

The paper discusses a simple multi-variable optimization problem: the bifurcation of a branch of a pipe of circular cross-section with a given initial radius r₀ and delivering a given mass flow rate m₀.The optimization is performed using an objective function [...] Read more.

The paper discusses a simple multi-variable optimization problem: the bifurcation of a branch of a pipe of circular cross-section with a given initial radius r₀ and delivering a given mass flow rate m₀.The optimization is performed using an objective function that prescribes the minimization of the entropy generation rate due — in this simple case — only to viscous flow effects within the tubes. Several fundamental simplifying assumptions are made to reduce the problem to a multi-variable optimization in three independent variables: the aspect ratio of the domain served by the flow, the diameter ratio of the primary and secondary branches, and the length of the secondary branch (the location of both the “source” of the fluid and the “sink”, i.e., the place of desired delivery of the fluid, being a datum).It is shown that the solution is strongly dependent both on the aspect ratio and on the diameter ratio, and that the "optimal" configurations display some resemblance to the branching patterns observed in natural structures. The study poses a challenge both to Designers and to Natural Scientists: are the optima suggested by the present procedure compatible with the structures currently used in heat exchangers and flow devices? Are they compatible with the structures observed in nature? No final answer is provided in this preliminary study, but a possible "falsification" procedure is outlined in the conclusions. Full article

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Entropy, Volume 12, Issue 8 (August 2010) – 7 articles , Pages 1855-1974

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