scholarly journals Reciprocally-coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis

2021 ◽  
Author(s):  
Charles W. Carter, Jr ◽  
Peter R Wills
Keyword(s):  
Free Energy ◽  
Historical Context ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Formal Structure ◽  
Second Law ◽  
Genetic Coding ◽  
Coupled Gating ◽  
Strange Loops

Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a “Chicken and Egg” problem; its resolution is concisely described by de Grasse Tyson: “the egg was laid by a bird that was not a chicken”. The concision and generality of that answer furnish no details—only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. The paradox in each example is resolved by coupling if, and only if, conditions for two related transitions between levels. One drives, and each restricts fluxes through, or “gates” the other. That reciprocally-coupled gating, in which two gated processes constrain one another, maps onto the formal structure of “strange loops”. That mapping may help unite the axiomatic foundations of genetics, bioenergetics, and catalysis. As a physical analog for Gödel’s logic, biomolecular strange-loops provide a natural metaphor around which to organize these data, linking biology to the physics of information, free energy, and the second law of thermodynamics.

scholarly journals Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 265
Author(s):  
Charles W. Carter ◽  
Peter R. Wills
Keyword(s):  
Experimental Data ◽  
Free Energy ◽  
Historical Context ◽  
Large Body ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Formal Structure ◽  
Second Law ◽  
Coupled Gating ◽  
Strange Loops

Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a “Chicken and Egg” problem; its resolution is concisely described by de Grasse Tyson: “The egg was laid by a bird that was not a chicken”. The concision and generality of that answer furnish no details—only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. In each example, a paradox is resolved by coupling “if, and only if” conditions for reciprocal transitions between levels, such that the consequent of the first test is the antecedent for the second. Each condition thus restricts fluxes through, or “gates” the other. Reciprocally-coupled gating, in which two gated processes constrain one another, is self-referential, hence maps onto the formal structure of “strange loops”. That mapping uncovers two different kinds of forces that may help unite the axioms underlying three phenomena that distinguish biology from chemistry. As a physical analog for Gödel’s logic, biomolecular strange-loops provide a natural metaphor around which to organize a large body of experimental data, linking biology to information, free energy, and the second law of thermodynamics.

First and second laws of thermodynamics: relationship, “inconsistency”, hidden effects

2020 ◽  
pp. 63-73
Author(s):  
A. M. Savchenko ◽  
Yu. V. Konovalov ◽  
A. V. Laushkin
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Second Law Of Thermodynamics ◽  
Second Law ◽  
Entropy Of Mixing ◽  
Ideal Mixing ◽  
Laws Of Thermodynamics ◽  
Relationship Of ◽  
The Relationship

The relationship of the first and second laws of thermodynamics based on their energy nature is considered. It is noted that the processes described by the second law of thermodynamics often take place hidden within the system, which makes it difficult to detect them. Nevertheless, even with ideal mixing, an increase in the internal energy of the system occurs, numerically equal to an increase in free energy. The largest contribution to the change in the value of free energy is made by the entropy of mixing, which has energy significance. The entropy of mixing can do the job, which is confirmed in particular by osmotic processes.

scholarly journals A thermodynamic approach to rate-type models in deformable ferroelectrics

2020 ◽  
Author(s):  
Claudio Giorgi ◽  
Angelo Morro
Keyword(s):  
Free Energy ◽  
Electric Field ◽  
Second Law Of Thermodynamics ◽  
Second Law ◽  
Energy Models ◽  
Polarization Electric Field ◽  
Field Plane ◽  
Vector Valued ◽  
Rate Type ◽  
Hysteretic Properties

AbstractThe purpose of the paper is to establish vector-valued rate-type models for the hysteretic properties in deformable ferroelectrics within the framework of continuum thermodynamics. Unlike electroelasticity and piezoelectricity, in ferroelectricity both the polarization and the electric field are simultaneously independent variables so that the constitutive functions depend on both. This viewpoint is naturally related to the fact that an hysteresis loop is a closed curve in the polarization–electric field plane. For the sake of generality, the deformation of the material and the dependence on the temperature are allowed to occur. The constitutive functions are required to be consistent with the principle of objectivity and the second law of thermodynamics. Objectivity implies that the constitutive equations are form invariant within the set of Euclidean frames. Among other results, the second law requires a general property on the relation between the polarization and the electric field via a differential equation. This equation shows a dependence fully characterized by two quantities: the free energy and a function which is related to the dissipative character of the hysteresis. As a consequence, different hysteresis models may have the same free energy. Models compatible with thermodynamics are then determined by appropriate selections of the free energy and of the dissipative part. Correspondingly, major and minor hysteretic loops are plotted.

scholarly journals The Effect of the Protein Synthesis Entropy Reduction on the Cell Size Regulation and Division Size of Unicellular Organisms

Entropy ◽  
2022 ◽  
Vol 24 (1) ◽  
pp. 94
Author(s):  
Mohammad Razavi ◽  
Seyed Majid Saberi Fathi ◽  
Jack Adam Tuszynski
Keyword(s):  
Free Energy ◽  
Protein Synthesis ◽  
Cell Size ◽  
Cell Biology ◽  
Second Law Of Thermodynamics ◽  
Underlying Mechanism ◽  
Energy Balance Equation ◽  
Second Law ◽  
Entropy Reduction ◽  
Unicellular Organisms

The underlying mechanism determining the size of a particular cell is one of the fundamental unknowns in cell biology. Here, using a new approach that could be used for most of unicellular species, we show that the protein synthesis and cell size are interconnected biophysically and that protein synthesis may be the chief mechanism in establishing size limitations of unicellular organisms. This result is obtained based on the free energy balance equation of protein synthesis and the second law of thermodynamics. Our calculations show that protein synthesis involves a considerable amount of entropy reduction due to polymerization of amino acids depending on the cytoplasmic volume of the cell. The amount of entropy reduction will increase with cell growth and eventually makes the free energy variations of the protein synthesis positive (that is, forbidden thermodynamically). Within the limits of the second law of thermodynamics we propose a framework to estimate the optimal cell size at division.

Models and Explanations: Understanding Chemical Reaction Mechanisms

2000 ◽  
Author(s):  
Barry K. Carpenter
Keyword(s):  
Internal Rotation ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Second Law ◽  
Original Design ◽  
Mechanical Analogy ◽  
Boston College ◽  
Chemical Reaction Mechanisms

In 1997, Ross Kelly and his coworkers at Boston College reported their results from an experiment with an intriguing premise (Kelly et al., 1997; see also Kelly et al., 1998). They had synthesized the molecule shown in figure 12.1. It was designed to be a “molecular ratchet,” so named because it appeared that it should undergo internal rotation about the A—B bond more readily in one direction than the other. The reason for thinking this might occur was that the benzophenanthrene moiety—the “pawl” of the ratchet—was anticipated to be helical. Thus, in some sense, this might be an inverse ratchet where the asymmetry dictating the sense of rotation would reside in the pawl rather than in the “teeth” on the “wheel” (the triptycene unit) as it does in a normal mechanical ratchet. Kelly and coworkers designed an elegant experiment to determine whether their molecular ratchet was functioning as anticipated, and they were (presumably) disappointed to find that it was not—internal rotation about the A—B bond occurred at equal rates in each direction. In 1998 Davis pointed out that occurrence of the desired behavior of the molecular ratchet would have constituted a violation of the second law of thermodynamics (Davis, 1998). With hindsight, I think most chemists would agree that Davis’s critique is unassailable, although the appeal of the mechanical analogy was so strong that I imagine those same chemists would also understand if Kelly et al. had overlooked the thermodynamic consequences of their proposal in the original design of the experiment. But now comes the interesting question: Suppose Kelly et al. had been fully aware that their experiment, if successful, would undermine the second law of thermodynamics, should they have conducted it anyway? Davis, in his critique writes: . . .Some would argue that this experiment was misconceived. To challenge the Second Law may be seen as scientific heresy (a nice irony, considering the Jesuit origins of Boston College), and the theoretical arguments against molecular ratchets and trapdoors are well developed. . . .

Mixing of Compressible Fluids

1961 ◽  
Vol 28 (3) ◽  
pp. 335-338 ◽  
Author(s):  
E. D. Kennedy
Keyword(s):  
Experimental Data ◽  
Compressible Fluid ◽  
Second Law Of Thermodynamics ◽  
Stagnation Pressure ◽  
Compressible Fluids ◽  
The Other ◽  
Second Law ◽  
Conservation Equations ◽  
Dimensionless Parameters ◽  
Constant Area

The problem of the mixing of two streams of the same compressible fluid in a constant-area duct is solved by applying certain dimensionless parameters first used by Kiselev. The extension to dissimilar fluids or to more than two streams is straightforward. Although the analysis is unrestricted, detailed results are given only for the case where one stream is sonic or supersonic and the other sonic or subsonic at the origin of mixing. For this case, the second law of thermodynamics indicates that, of the two solutions of the conservation equations, the subsonic one is always permitted while some of the supersonic solutions are thermodynamically impossible. Upon examination of experimental data, it is further concluded that of the admissible supersonic solutions, only one may be expected to occur. The establishment of this supersonic solution with its relatively high stagnation pressure leads to the conclusion that when the initial temperatures are sufficiently different, there exist thermodynamically possible solutions with a stagnation pressure higher than that of either of the two initial streams.

It's about Time: The Temporal Evolution of Order

2009 ◽  
Vol 34 (2) ◽  
pp. 131-137
Author(s):  
MOSHE PERLSTEIN
Keyword(s):  
Temporal Evolution ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Second Law ◽  
Ethical Values ◽  
Other Hand ◽  
Measure For Measure ◽  
Analyse Time

This article borrows its methodology from physics in order to analyse time in the theatre as evolution of order. Two set designs (both designed by Roni Toren for the Khan Theatre in Jerusalem) are portrayed through this perspective, representing inverse examples. In Measure for Measure, directed by Gadi Roll, the temporal evolution of space is from order to disorder, obeying the second law of thermodynamics. On the other hand, in The Seagull, directed by Ofira Henig, the evolution contradicts that law. The problem of depicting disorder on stage, the possibility of such a contradiction, the implication of the two different perceptions and their ethical values are discussed to prove the effectiveness of a methodology adopted from physics.

scholarly journals Distinguishability of non-orthogonal density matrices does not imply violations of the second law

2019 ◽  
Author(s):  
PierGianLuca Porta Mana
Keyword(s):  
Hilbert Space ◽  
Density Matrix ◽  
Thermodynamic Analysis ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Second Law ◽  
Density Matrices ◽  
Matrix Space ◽  
Von Neumann ◽  
Quantum Thermodynamic

The hypothetical possibility of distinguishing preparations described by non-orthogonal density matrices does not necessarily imply a violation of the second law of thermodynamics, as was instead stated by von Neumann. On the other hand, such a possibility would surely mean that the particular density-matrix space (and related Hilbert space) adopted would not be adequate to describe the hypothetical new experimental facts. These points are shown by making clear the distinction between physical preparations and the density matrices which represent them, and then comparing a "quantum" thermodynamic analysis given by Peres with a "classical" one given by Jaynes.

scholarly journals A General Solution to the Different Formulations of the Second Law of Thermodynamics

2021 ◽  
Vol 82 (2) ◽  
pp. 61-71
Author(s):  
Saeed Shahsavari ◽  
Mehran Moradi
Keyword(s):  
General Solution ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Second Law ◽  
Energy Structure ◽  
New Approach ◽  
General Physics ◽  
Classical Thermodynamics ◽  
Physical Laws ◽  
Energy Components

The second law of thermodynamics is one of the most important physical laws that has been extracted by different formulations. In this paper, a new approach to study different formulations of the second law is extracted based on the energy components of the system as well as introducing the independent and dependent energy components concepts. Also, two main formulations of classical thermodynamics, and also entropy from the perspective of general physics are discussed based on the energy components of the system for constant applied energy to the system in different conditions. Kelvin-Plank and Clausius formulations, as two main classical formulations, are all assertions about impossible processes. Considering the energy structure equation of the system, as an equation to formulate the performed process using activated energy components, it is shown that different formulations of the second law of thermodynamics represent the same concept in the perspective of the energy structure. Finally, a new general formulation to the second law, based on the energy structure of the system is extracted, and the equivalence as the other formulations is shown. The presented formulation is extracted based on the dependent and independent activated energy components, and in fact, shows all possible paths in the considered energy applying to the system.

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